Assets in bundles are different from original

Hi, I've started using asset bundles and I notice that my assets built in asset bundles are slightly different from original assets. For example, some of my prefabs lose script attached to them, or transforms don't have the same values (position, rotation). Seems like my asset bundles are somehow corrupted but after few times refreshing and cache clearing, I still get the same outputs. Please help.

I'm using Unity 2018.2.9f1 with customized asset bundle browser (which I don't think it affects any outputs though). I pack lots of assets such as prefabs, sounds, fbx files, etc. which are included in separate asset bundles (maximum size is ~15mb I believe)

PS. I cannot attach any picture captured from our project

Thanks in advance