misalignment of some UPHENO terms with BFO?

[RLWOHIO]

I recently merged upheno with a number of domain ontologies and ended up having a massive number of unsatisfied terms. They were primarily due to their alignment with BFO_0000003, BFO_0000004, BFO_0000040, and UBRON_0001062 as superclasses. For example, UPHENO_0000519 has BFO_0000003 as a superclass. I am not sure if this is consistent with its own logical definition: has part some (delayed and (inheres_in some embryo implantation) and (has modifier some abnormal)), where delayed (PATO_0000502) is a process quality and should be a subclass of BFO_0000020. Similarly, UPHENO_0001150 has UBERON_0001062 as a superclass yet it is defined as: has part some (increased size and (inheres_in some extraembryonic membrane) and (has modifier some abnormal)). I don't see how a phenotype like "increased size" is a subclass of UBERON_0001062. In both of these examples, the focus should be on quality, not bearer, right? After all, UPHENO is about capturing phenotypes. All the unsatisfiable UPHENO terms were resolved after deleting the three BFO terms and/or UBERON_0001062 as their superclasses.
Am I missing something here?