Physics2D.BoxCastAll not registering hits

So, I can't use the inbuilt Physics2D engine since my objects' movements can be interrupted and buggy when leaning on it. This means I've had to make my own collision system.

So far movement is okay, I can collide with the terrain I generate fine. However, I can't have objects collide with each other.

I've heard there are issues when moving objects via scripts instead of via physics, but I've not found a workaround.

I have situations where BoxCastAll may have a "zero direction", zero distance, or will be casting away from should-be hits.

Long story short, BoxCastAll is not returning all hits. What am I doing wrong, and how would I go about fixing this?

EDIT: Just tried using OverlapAreaAll and it is, similarly, not returning any hits.

Also, it appears that it doesn't only occur on the possible earlier corner cases, sometimes hits just don't register at all in random conditions.