Several objects were made in Illustrator and exported to SVGs.
Later they were imported back into Illustrator.
Please take a look at both the GIF and the file atached.

When one tries to select all the top-level groups and align them to left — it doesn’t work.
Aligning to center and to right works, but once these get aligned to right — aligning to center stops working too.

When exploring layers, it’s clear that these groups have something else inside besides rectangles — but only in Layers, not on canvas. These can’t be selected or changed, only rearranged, renamed, deleted.

When these get deleted, aligning works as expected.
If just ungrouped, aligning works as well.

If I recall, these are empty groups that Illustrator automatically deletes if a group has no children, but keeps when imported from an SVG, where these are allowed.

I recall even more faintly that there was another related report about these phantom objects, but can’t find it.