The big problematic incompatibility I see between Dark Mirror
and the rest of the canon is that in Dark Mirror
, the Mirror Universe's existence was kept secret by the Federation, whereas in "Crossover"
Bashir learned about the transporter accident at Starfleet Academy.
I just checked MB, and apparently Dark Mirror
took place in 2367. IIRC, DS9 was Bashir's first posting after the academy, and he was posted there in 2369. So as long as Starfleet Command declassified this information after Dark Mirror
but before Bashir graduated, both could still be true. (Maybe it was the Dark Mirror
incident that caused
Starfleet to declassify the original crossover!