One of the goofy idiosyncrasies of MM is I've said before the item context area. Anything you can bottle or the deeds and peculiar items weirdly need to be in an exact spot to be used correctly. In the deku palace it's very easy to miss sprinkling the spring water on the magic bean sprout, in the great bay observatory you will repeatedly have to inch around to find a place to drop the eggs(and even sometimes standing in that place will only allow you to drop 1 egg so you have to move again), and in the deku houses when using bugs you have to be standing in the right spot for them to travel to the soil. Now in both OOT and MM bugs will very rarely wander off but in MM they allow you to only need 2 of the 3 bugs rather than needing all 3 in OOT, however if you don't drop the bugs in the right spot in MM they will refuse to go the soil entirely whereas in OOT they will always go to it when in proximity
So I have grabbed multiple bugs ahead of time to avoid wasted time. If you play this yourself, remember to smash your face against the wall right where the soil patch is before releasing the bugs