Yukari's limits aren't clearly defined (mostly because it would be impossible to define an actual limit because of the scope of her ability), but you can make speculations and good guesses based on observations.
-As said above, she likely would not be able to create a barrier as strong (or as complex) as the Great Hakurei Barrier (by herself). Of course that's pretty ambiguous though, so all it says is that Yukari has limits and wouldn't be able to create/remove the whole barrier on her own.
-Yukari was not able to break the barrier surrounding the Lunar Capital for a while because the barrier was very complex. This implies that the complexity of the boundary affects how feasible and timely it is to manipulate, or possibly how long it takes to figure out.
-The only time Yukari can create a gap to the Moon is during a full moon, through its reflection on a large body of water (or something similar). This is because the boundary between the Earth and the Moon then comes into existence, through the reflection. Likewise, to get back from the Moon she could go through the reflected Earth on the Moon's ocean. The "Lunarian sage's" trap on the Moon demonstrates that the boundary is constantly being affected by the period of the Moon, and can close itself. This says many things, including that some boundaries can only be manipulated when they actually exist in some manner and are connected by something, that the situation can affect the existence of such boundaries, and that she can't just gap whereever she wants.
-The sage's trap also reveals that Yukari is not immune to foiling; she can't just manipulate boundaries to sync up the Moon to 30 days and things like that just because she wants to. Additionally this reveals that if there's ever anything that Yukari cannot do, it shows many more limitations than the deed itself, since she also isn't able to manipulate the boundaries necessary to circumvent the problem. Again, this implies that boundaries take more effort than others.
-This also implies that manipulating one boundary can affect another, which is supported by Reimu's Phantasm dialogue when Yukari points out the Reimu undermines how many barriers she would need to fix. Manipulating a natural law must mean that she also must manipulate a natural law related to the first, and so on. As such, Yukari's ability is likely extremely strenuous to uphold. Manipulating complex boundaries probably takes an enormous amount of energy. This is speculated to be the reason why she sleeps so often and requires shikigami to do a lot of work for her when possible.
Although, Yukari's intelligence and status pretty much makes up for these limits. There are probably others but I don't want to go search for any more.