Windows 2012 Server compatibility
There are a number of different ways that Samba can be considered compatible with Windows and so this page attempts to try to explain some of them (and which ones might be regarded as important). A number of these details will obviously apply more generally to other Windows versions.
SMB protocol features
As Windows 2012 (and 2012 R2) ships with a particular version of SMB, clients which expect to negotiate a certain version may see differences between Windows and Samba. SMB allows for many optional features which are negotiated and servers generally support multiple versions of SMB for interoperability with different clients. This means that servers and clients will speak a wide variety of flavours of SMB, meaning interoperability issues with Samba are generally limited to individual applications and use-cases which have stricter requirements on their SMB connections (encryption and supported ciphers, resilient handles).
RPC server features
This is similar to SMB, many calls or structures have been deprecated over time. In many cases Samba does not implement every call, or has calls which do nothing. There may even be entire RPC pipes which are unimplemented, although their functionality is reproduced in some other way e.g. eventlog6 logging.