@DokiDokiTsuna
the journey of apprenticeship and 'learning a trade' was a STAPLE of fantasy fiction
Except that it’s not exactly a staple and more of just one of the tropes, I don’t even recall that trope being used much in LoTR, Dragonlance, Witcher, Conan and many other influential works; this trope seems to be abused all the way in fantasy like JRPGS with very young protagonists.
whether or not it 'deserves' to be stereotypical
Simply put, yes it does, because most fantasy in a traditional sense is derived from LoTR so most people assume medieval setting when they hear the word “fantasy” without any prefixes, this is literally what stereotype is.
For one thing, I think logic-breaking elements are quite common in ALL fantasy, just like they are in sci fi...that's why 'suspension of disbelief' exists.
First of all, logic-breaking happens when you introduce a rule and then do something that contradicts it or when you introduce several rules which contradict one another; fantasy elements can easily break realistic logic but cannot break a custom one as long as it doesn’t contradict itself. “Urban fantasy” logic usually contradicts itself when realistic and custom rules are just mashed together without any attempts to make them work together.
Second, suspension of disbelief is when you don’t explicitly explain every single rule and rely on events to look plausible based on rules you did explain and rules people assume by default; in a quasi-realistic setting the default is, well, a real world, so when someone just throws in random elements without even trying to make them work together the whole thing becomes, as you’ve called it, “a skill issue”.
to work realistic elements into a fantasy world
...Which is exactly the opposite of “urban fantasy” because it’s essentially adding realistic elements into a more abstract setting to make it feel more plausible.
@Tubacabra
how can it be possible to "break the logic of [your] world"?
If we are talking about “urban fantasy”, it usually relies on a quasi-real world setting which brings a very strict set of rules and limitations and throwing in random fantasy element should change the whole set completely but in most cases it doesn’t, everything stays exactly the same as in a realistic setting except that one element which creates lots of contradictions where realistic logic clashes with custom logic; you can’t just put a giant flying lizard into a modern setting and expect everything to function exactly as it was without it. Yes, technically you can change the world logic in accordance with the newly introduced element but that will require so many changes it will stop being an “urban fantasy” and will become just a regular fantasy in a quasi-modern setting.
If we are talking about “your world” which implies custom logic, your rules must not contradict each other and you shouldn’t do anything that contradicts these rules. The most notorious example of breaking the logic is a Mary-Sue character which doesn’t follow the established set of rules and\or bends the whole system in its favor.