Hi @Zach_Burcham - having a plot showing the results could help us better answer this question.
clr coordinate do not necessarily imply increase / decrease (since it is not possible do this in the first place). Instead, these coordinates represent log-fold change relative to the average microbe.
So it is possible that both taxa are higher, but one of them is increased greater than the average microbe and the other is increased less than the average microbe (provided that the average microbe is also increased between these two conditions).