Thank you for the explanation. I'm not very well aware of the specifics of Lego construction, personally, so this is very much appreciated. I found a few more, actually, this time on a set I don't own a physical copy of - the MX-81 Hypersonic Operations Aircraft:
The first one shows up on Page 52 of Book One. The previous several pages have asked me to create a fairly large structure which I need to attach "vertically" to some Technic pegs. It's difficult to explain, but the way the thing is designed has two half-peg/half-axle things (43039) fit inside two 15-hole Technic beams (64871). Directly behind the beams is a stack of several blocks. The structure also has a couple of 1x4 plates (3710) underneath it, supposedly coming down to the same "level" as the half-axel things. I presume it works in real life since it's in an actual real set manual, but it doesn't work in LDD. The lower plate collides with the block wall when you attempt to place the structure. In this case, the solution was simple - I removed the lower 1x4 plate and the thing fit like a glove. In fact, I have to wonder why the lower plate is even there, since it doesn't seem to serve any real purpose.
The other shows up on Page 43 of Book Two. The previous page had me build a "windshield" structure, complete with a white shell (45705). That's the part with the actual issue, because the manual next asks me to lower this down on top of a triangular sail-looking thing (51000). The idea is that the narrow tip of the sail thing would fit into the hollow "inside" of the shell... Except it doesn't. Purely visually in LDD, it's clear that there's plenty of room in there, but the shell's collision box doesn't seem to acknowledge the piece's internal space, treating it like it has a solid flat bottom. I solved this by bending the sail thing "inwards," which allowed me to bring the shell down as far as the manual would want, but even then the shell was colliding with nothing at the far reach of its pivot.
There was one other one, but upon revision, it turns out that was my fault. Oops!