Sometimes when using bots to lay foundations a building will be exempt from the module bonuses. I can usually fix this by removing the refined concrete under the building and then just placing it again. I haven't noticed this happening while placing foundations by hand. Is there maybe a setting I should try changing to counteract this?

I can't seem to replicate this (tested with concrete + assembling machines), does it happen for every building placed down by a bot or at random? Does it occur with bots in power armor or roboports? A video/gif showing the bots placing the affected buildings would be nice.

It happened with bots from roboports. Also the assemblers were already placed, when I add the refined concrete afterwards some of the assemblers don't get the bonus. A small number, like two in twenty assemblers don't get the bonus. The rest work fine
This might be because of the module inserter mod, I noticed that when I upgraded the modules from tier two to tier three using the mod and bots, the assemblers updated and applied the bonus correctly.

I'll try and capture a video/gif for you. Is there a specific place I can upload the video?

You can upload them on imgur or streamable

Found how to reproduce that and source of problem:
When you build machine with modules, then here https://github.com/Dummiez/Factorio-StableFoundations/blob/main/control.lua#L242 we can match not a assembler, but special entity called "item-request-proxy" (have same type "item-request-proxy"), which shows that modules are requested.
Also we can match "construction-robot"

The most simple fix: remove following "break"