The first thing I would questions is why shoot 24.000 for a 25.000 delivery unless you have 23.976 and DCP deliveries as well.
And if that is the case, I question why record 25fps TC on audio when picture is a 24 – those should be the same to make post a little easier.
And with all that being said – try importing the 25fps TC audio into the 24fps project. Audio does not have a frame rate other than a rate defined by calculating samples from midnight. You will be prompted for a frame rate when importing, choose 25, MC will recalculate for the 24fps project and see if your errors go away.
Issue here is that timecode will get converted so EDL’s back to original BWF files will not be correct. You can change all the timecodes within the files (I recommend on a copy) to 24 using Sound Design’s WaveAgent. The import into MC. Wave Agent allows TC to be recalculated or not. See which one best fits your needs. Speak to your audio post folks if possible.
Michael