Man, oh man, Suffice to say, finding sources on a niche topic like this were NOT easy, but they do exist! At least a few Dermatologic studies were published after the war and I was able to find a few of them, both of which focus on Acne in the Pacific Theater. While prior to the war acne was considered a nuisance more than something serious, American servicemen in the Pacific were found to be developing what came to be called "tropical acne", an extreme manifestation of the condition that could be physically debilitating and symptoms of which included "large pustules, draining sinuses and extensive, disfiguring scars,frequently keloidal". To be sure, it isn't that the breakouts themselves were being caused by the men simply being in the Pacific - the studies indicate that a history of acne previous to service was a major factor - but various factors from the wartime environment, including "increase in vasomotor activity, caused by the heat, plus the inadequate toilet facilities" all contributed to severely affect men who had been sent to the Pacific. Being unable to clean, minor outbreaks could become infected, and many cases seem to have been serious enough that that the afflicted men were unable to continue serving on the front and had to be evacuated for more medical treatment, and many declared permanently unfit for duty.

Not all men who suffered breakouts were necessarily suffering from such acute symptoms though, and all in all, acne seems to have been one of the more common issues soldiers in the Pacific theater faced. As far as dermatological issues, at least, it was second only to tropical skin disease/fungal infections, with somewhere between 20 to 30 percent of all patients hospitalized for skin issues suffering from tropical acne.

As far as treatment goes, doctors found that standard treatments were generally quite ineffective and remaining in tropical conditions would generally cause a worsening. Attempts to use penicillin showed little real result while evacuation to cooler environments alone could cause real improvement in the condition, so that seems to have been the standard procedure.

So in short, someone else can weigh in on other theaters, but at least in the Pacific, Acne was a serious issue faced.

Edit: I was able to find one other source, which doesn't add to much to what has been said here beyond the small addition here but does note that as far as the European theater goes "[acne] was a condition of no consequence".

Edit II: The book also includes a picture of tropical acne if you want to see what we're talking about. I don't want to link directly to it for the RES people so you don't open it automatically by accident, so scroll on down to Illustration 85 in the Table of Contents.

Cohen T.M, Pfaff R.O. Penicillin in Dermatologic Therapy: Report of Results in One Hundred Cases. Arch Derm Syphilol. 1945;51(3):172-177. doi:10.1001/archderm.1945.01510210014002

Novy F.G. A Severe Form Of Acne Developing in the Tropics. Arch Derm Syphilol. 1949;60(2):206-216. doi:10.1001/archderm.1949.01530020074011

ETA: Heaton, Leonard Dudley, comp. Infectious Diseases and General Medicine. Edited by Robert S. Anderson. Vol. 3. Internal Medicine in World War II. Washington: US Government Printing Office, Division of Public Documents, 1968.

I may actually have a relevant answer to this! For full disclosure, I'm not a historian and this is my first response to an AskHistorians thread, so if I mess anything up I hope my post is justly smote.

If I'm allowed to rephrase your question a bit to give it a broader context, it seems that what you're asking, more generally, is: did soldiers in WWII, in the course of being soldiers, find themselves in conditions that led to painful blemishes or skin irritations?

While this might not specifically mean acne as you're imagining it, the answer is, undoubtedly, yes! My grandfather, now deceased, served in the 6th Emergency Rescue Squadron, one of seven squadrons of the USAAF (the United States' air division before the creation of the USAF in 1947) designed for autonomous rescue during WWII. Here's some brief verification of him to validate the source. In looking at your question, I recalled a story he once told of a soldier laying on his stomach on a bed who was receiving injections to treat a pilonidal cyst, to which my grandfather asked "what's that?" and the soldier responded, "it's a thing on your butt!" Unfortunately, without any sort of documentation of this treatment or exchange, it's purely anecdotal for the purposes of your question.

However, I can do better!

As it turns out, in researching more specifics on what pilonidal cysts are, I discovered that it was actually such a common occurrence during World War II that it had a name: Jeep Riders' Disease (or just Jeep Disease).

So before we get ahead of ourselves, what exactly is pilonidal disease? According to the American Society of Colon and Rectal Surgeons, pilonidal disease is a skin infection in the crease of the buttocks, close to the coccyx, which can become an inflamed, painful cyst and may also become infected. I don't think it's a stretch of the imagination to see how this could be bad for soldiers - discomfort and pain while moving or sitting would be present, and the treatment, which would likely involve phenol injections or lancing and drainage, could leave victims bedridden for days. There's also considerations for the potential for infection and sepsis - soldiers are going to be moving through dirty, hot environments that are going to aggravate their condition by sweating and the inability to bathe regularly. Though the initial question seems to be one of beauty, I think it's imperative to consider the implications of skin conditions that won't just be unsightly, but taking soldiers away from active duty.

Which brings us to the question of prevalence. Was this common? Most articles I've found, such as this one seem to lead back to the same place: A February, 1944 article published in the Southern Medical Journal called Jeep Disease: Pilonidal Disease of Mechanized Warfare. Although I can't personally access the article, other articles citing it make the claim that about about 80,000 soldiers during WWII were hospitalized for pilonidal disease due to long and frequently-rough jeep rides which put pressure and irritation on the coccyx of soldiers, hence the name Jeep Riders' Disease. Indeed, a study that occurred from 2005 to 2011 found that, even today, pilonidal disease retains a significant association with military personnel. Even though my grandfather's story will never be the primary source that I wish it were, it seems like he may not have been too far off the mark about this condition affecting soldiers during WWII.

So, to get back to your original question: Was acne ever an issue in WWII? To the degree we're talking about facial blemishes or irritating marks, I can't speak. But if we ask more broadly about the kinds of conditions that soldiers worked and fought in, could we say that they contributed to health issues, especially of the skin, which could impact service? Definitely. In the case I've described here, perhaps the soldiers have a great complexion, but it's what you don't see that's the real problem. While I find the question of whether acne as you imagine it would be common a good one, I think there's definitely enough information to say that there were skin problems in World War II, caused by the conditions soldiers were in, that were not only unusual or annoying, but downright painful and dangerous.

Short answer: Yes, it was an issue.

Long answer: Acne, and skin disease in general, were evaluated in new recruits and draftees when they first reported for service. However, there was no official policy on whether to accept or reject someone based on their skin disease(s). Many doctors, especially early in the war, leaned towards accepting those with diseases. This accepting policy would prove to be somewhat of a mistake, because it became apparent that these admitted men were a large burden on Army dispensaries and hospital facilities. This burden was amplified when deployed into Tropical areas of combat, further reducing the combat effectiveness of the afflicted soldiers.

Acne in and of itself was not used as justification to turn people away however. Of 20,000 candidates for induction at U.S. Army Recruiting and Induction Station, Tacoma, Washington, 248 had acne vulgaris, and 0 were rejected.

Going back to the Tropics, acne (and other skin diseases caused by the tropical environment) was a significant issue.

From a survey at Fitzsimons General Hospital:

"A typical history revealed that the patient had had some trouble with blackheads and acneiform lesions when he was 15 to 18 years of age, but none since, including his period of training in the Zone of Interior. Trouble began, however, some 6 months after his arrival in the Southwest Pacific Area or some other tropical area. The first manifestation was the development of large, tender, inflammatory cystic lesions on the shoulder and back, which made it impossible to carry a pack. After he was treated for a considerable time by the battalion surgeon, sometimes in a forward hospital and occasionally in a general hospital, the patient was evacuated to the Zone of Interior."

The severe acne developed by men in the Southwest Pacific Area and India-China-Burma theater was very painful and risked life-threatening infections should a lesion burst and be exposed. the best course of action became immediately sending the men to the Zone of Interior (i.e. back to the U.S.) when they developed acne too severe to be combat effective, as military hospitals were not equipped to deal with it.

Source: http://history.amedd.army.mil/booksdocs/wwii/internalmedicinevolIII/chapter20.htm

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When I would go to boy scout camp for a week and not shower at age 12-15, my acne would disappear. Working that hard and sweating all the time clears your pores.