I would suggest that you contact Support for this issue but, prior to doing so, read carefully through the special allocations demo in the program (although what you are seeing could be a coding issue).
https://ttlc.intuit.com/community/using-turbotax/help/what-is-the-turbotax-phone-number/00/25632
I would further suggest that you seek professional guidance (e.g., an in-person consultation) for the 1065 return at this point. The reason being is the return is now considerably late as 1065 and 1120-S returns were due March 16th (those returns were not extended) and there are penalties for a return filed after the due date.
