Hi, are the loaders supposed to not work on trains? I usually use the miniloader mod, but now that Beltboxes added the compact loaders aswell it felt redundant to have both.

Miniloaders work on trains. Is there anyway to disable to loaders if thats is the case so that I can go back to using miniloaders?

Yup - vanilla loader entities don't work on trains, Miniloaders work around this (and allow circuit conditions) by adding very fast invisible inserters in addition to the loaders. The loaders that this mod adds can be disabled in startup options if you prefer to just use miniloaders.