Three important Khans of the Golden Horde in the 14th century were Toqta, Özbeg Khan, and Janibeg Khan. At least that's what appear to be their commonly accepted names, there's a thousand variants to them it seems.
Now, the most obvious difference is that Toqta was just, well, Toqta. His successors were Özbeg Khan and Janibeg Khan. Instead of just Özbeg and Janibeg. Am I reading too much into this, or is this perhaps a misunderstanding and Toqta was also known as Toqta Khan?
Also, follow up question: What's the meaning of Janibeg and Özbeg both ending in -beg?
Yeah, this seems like a misunderstanding on your/your sources' part. In all three cases, "khan" is strictly used as a title placed after the last name, in accordance with the rules of Turco-Mongol grammar. Toqta's name was just Toqta—just like Özbeg and Janibeg are those respective rulers' names—but "khan" would typically be added to the end as a marker of respect and recognition of the ruler's title. (This is similarly true for other Turco-Mongol rulers—Kubilai Khan, Sultan Süleyman Han, etc.) This is how they're usually referred to in chronicles, diplomatic missives, and other contemporary sources.
This is not to say, however, that titles were always totally separate from names! Your followup question speaks to that point quite nicely: "beg" was also a title (used by the early Ottomans, among others), but cases like Özbeg make more sense if we read it as part of a composite name. (Etymologically speaking, Özbeg means something like "lord of oneself"—if we split off the "beg" and read it as a separate title, it would be "Lord Self.") "Sultan" was another title that was common as a composite name particle—for example, in the name of the celebrated Timurid prince and patron Sultan-Husayn Bayqara.
Eventually, "khan" too began to be used as a name rather than a title (and remains a popular surname among Muslims in India and Pakistan). But in the time of the Golden Horde, it would have still been received as a title, and moreover one which usually signified direct descent from Chinggis Khan. I talk a bit about the nuances of "khan" in the context of Islamic titulature here.