I've recreated this issue on two of my survival worlds a few time.
1st world 5 allays holding honeycombs in an enclosed area.  My nether portal is in a separate enclosed area of my base.  When I stepped through the portal, the allays appeared in my nether base.  When I stepped back through to the overworld, the allays were in the same area as my portal.  The allays were no longer in their original location.
2nd world 3 allays.  2 holding dirt in a glass room with no openings.  1 holding an apple in a outdoor tree farm.  When I step through the nether portal, all 3 appear in the nether base and when I come back through they are in the main part of the base, not in their normal areas.