The most likely explanation for your problem occurs when two files are copy and pasted in Windows Explorer windows. It is very important that this method of creating duplicate parts is avoided.
Alibre Design assigns a hidden variable, a global unique identifier, to each unique item created in the program. When one of those items is copied in Windows Explorer, both items then share that identifier, and it is therefore no longer unique. If an assembly then references parts with the same identifier, it may become confused and change all pieces to the original.
If you need to create duplicate parts or copy Alibre Design files, first, open the original part in the program, and save them with a different name using the Save As command. You can then likely solve your assembly issue by opening the assembly space and simply right-clicking the troublesome part and using the Replace Component command. This will create a unique identifier and fix the issue when it replaces the similar part in your assembly.