Yaaay, I fixed it. As many in the comments here allude to, the problem was with dependency detection between "losing all abilities" and any effect that gives an ability if you have some ability (e.g. Sephara, or Kwende).
Because no dependency was detected, the effects assumed that the application of one of them would have no impact on which objects were affected by the other. So Sephara and Frogify both started thinking they applied to Alela, and after Frogify applied Sephara didn't recheck.
Detecting the dependency fixes the issue. Our next GRE patch is still a ways away, but this will be fixed in it. #wotc_staff