There could be a number of reasons for this issue; the most obvious being that you just haven’t completed the mandatory metadata on your document before checking it in. However, I am assuming you are a little more cluey than that.
If you are dealing with a MS Office document (particularly Excel) and you are being diligent and filling out the required metadata in the DIP, saving and then trying to check it in and you are still being told you haven’t completed all the required metadata then I suspect the problem may be with Password Protection on the document or a workbook inside. Here is a good little summary of the issue.
The work around, while the desktop guys scramble around trying to tweak the group policy, is to close the document without checking it in, navigate to the document in the SharePoint document library and then Edit the properties of the document and set them in the Edit Metadata Form. When satisfied, check the document in via the library ribbon. Unfortunately this must happen every time the document is checked out for Edit. The same properties will always be wiped by the check in. If you can just turn off Protection on the document then that will stifle the issue as well. Depending on the business requirement, this may not be appropriate though.
Alternatively if Password Protection/Encryption is not your problem, then I must ask you whether you are using Lookup lists values as metadata in your document library? If so, make sure that the users trying to fillout the metadata and check the document in actually have sufficient access to the source Lookup list. If they don’t, they won’t be able to complete that piece of metadata.