I don’t believe it should only trigger if a single loop node exceeds the limit, as for example you could have a sequence of nodes, which are called over and over again, without any loop, for example recursive calls.
You can also see that UE4 does not count loop iterations (but some other internal instruction count) just by looking at the ForLoop macro: it’s a normal macro, nothing special in it.
If you trigger the MaximumLoopIterationCount, just simply increase it in the Project Settings. The naming might be ambiguous, as it is not actually working with loops, it’s probably something like this internally: “If we reach X instructions, then we’re probably in an infinite loop, so let’s stop here”.