Belisarius clearly had quite some trouble with his fellow/subordinate generals.

At the time each general commanded a personal army of bucellarii, so disagreement quite literally meant dividing the army. The resulting lack of co-operating no doubt contributed to Byzantine defeats in both Italy and the Middle East. David Alan Parnell describes this well in his article The Social Networks of Justinian’s Generals in Journal of Late Antiquity Volume 8, Number 1, Spring 2015

Belisarius had a circle of generals around him. The ones we know by name are Valerian, Cyprian, Martin, Ildiger, Uliaris, and a John the Glutton. They famously butted heads with Narses the Eunuch and his circle, whom we know included John the Nephew of Vitalian, Justin, and the brothers Aratius and Narses. The conflict nearly lead to the loss of Ariminum in 538, lead to the loss of Milan in 539, and greatly hampered the later efforts against the Goths when John the Nephew of Vitalian and Belisarius refused to co-operate with each other. Of mention is also Belisarius' mistake in picking the generals (of his own faction who were loyal to him) to relieve Milan. Though Procopius gloss over it, he relieved Uliaris for the debacle even though the man had served Belisarius loyally for many years.

Procopius also off-handily mentioned a third general/faction hostile to Belisarius, a certain Bessas who was sent away from Ravenna in 540 even though there's no evidence he was tied to Narses' group. Indeed he came to Italy with Belisarius in 535 so he should've been closer to Belisarius.

When Belisarius was sent to fight the Persians in 541, he also butted heads with a certain Peter the General and a third John who commanded troops from Mesopotamia. Though details are scarce (probably because Procopius wasn't there to witness it) but the resulting disagreement again lead to defeat. And in 542, John the Glutton went to Peter's side and together they had Belisarius recalled to Constantinople.

Parnell points out that it would appear at the time all generals were of the same rank, the magister militum, and Justinian rarely clarified the command structure. This must have contributed to the lack of unity. There are mentions of other such conflicts in other areas, so there's no doubt this structure made Belisarius' command difficult. However Parnell also reminds us personalities must also contribute to the split.

Not mentioned by Parnell but relevant to this topic is the conflicting report of what happened at Callinicum in 531. Procopius says Belisarius was goaded by his army into fighting, and al Harith and the Arabs fled the field on contact, leading to the rest of Belisarius' army being outflanked. Belisarius bravely dismounted and commanded the rear guard. John Malalas' chronicles however says that though some Arabs fled, al Harith held firm. Belisarius was the one who fled as soon as things turned south, and the brave dismount and rearguard actions were by the generals Sunicas and Simmas. We don't know who's right, if either one. If you believe Procopius, then Belisarius lacked control of his army. And on a separate occasion Procopius does mention when Belisarius went to Carthage to suppress a mutiny of the army there, his own troops in Syracuse decided to mutiny, too. If you believe Malalas, then Belisarius in this instance was a coward. For what it's worth, John Bury writing over a century ago is of the opinion that "the adverse witness seems the more credible and is generally the more trustworthy of the two", and after sending the general Constantiolus to investigate the defeat, Justinian recalled Belisarius and seemingly no one else.

So what are we to conclude? Well Belisarius was no doubt good, considering his victories. And the tasks presented to him were by no means easy. However, he made his share of mistakes, have his flaws, and had his share of defeats. And it would seem that many of his superiors, fellow generals, and subordinates at one point or another had negative opinions of him. Procopius, our main source on the man, is also one. He started his About the Wars as extremely pro-Belisarius, but slowly becomes more and more disillusioned with the general until he decides to vent everything in his Secret History and choose a new hero for his later sections of the Gothic Wars. So I would say his reputation as a military genius is very much a product of later times, and it doesn't match our records.

Special thanks to /u/shlin28 for recommending the article the last time Belisarius came up at /r/badhistory. Quoting him from a previous Askhistorians thread

I had no idea that Belisarius is revered by military historians. He was clearly important, but his fellow generals Narses and John Troglita were in my opinion just as skilled and certainly more important in securing the long-term stability of the western territories Belisarius reconquered (kind of, I don't think we can give the credit for winning Italy to Belisarius). I think most of Belisarius' reputation comes from the fact that his client, Procopius, wrote the most extensive secular history of the sixth century, which glorified Belisarius' earlier victories and minimised his defeats. It gets more complicated for the events of the 540s and 550s, when Procopius became disillusioned with Belisarius, but his later career isn't so well-studied and isn't nearly as prestigious as his earlier career anyway.
[Omitted]
From my perspective, Belisarius was certainly not anything like Alexander the Great, even though he did win several major battles. At a strategic level, he was not able to secure the loyalties of the locals or win miraculous victories when he did not have a material/political advantage. He also allegedly had a weak personality, being rather naive and trusting of his adulterous wife, if we believe the scandalous tales spread by Procopius in his Secret History. Unfortunately, Procopius is our main source for this period, so the image we get is rather schizophrenic, that of a young and successful general plagued by a whole host of personal issues. In reality, Belisarius was probably much more mundane, which for me makes him all the more interesting to study.