Selector tool glitch — element selected and deselected at once
Sometimes, elements will incorrectly be deselected, getting them into a strange state where they are seen as unselected in the layers panel, but being displayed as selected on the canevas. Most operations will not affect it (move and scale), but some, including align, will produce strange, incoherent results. It either stops at random or does not, needing a restart of Illustrator to be able to resume editing.
It has happened multiple times already over the last weeks, and I cannot see a pattern to it's occurence. Just now it happened while navigating the history where elements were being grouped/ungrouped and transformed multiple times.
Please accept my sincere apology for the inconvenience. Please get in touch with us at any of the other support channels – https://helpx.adobe.com/support.html . Since this is not a generic issue that we can reproduce at our end, we will need someone to look into your machine to figure out what is going on here.