It seems that after the new update, the Mana Well objects (consisting of base, crystal bag and symbols parts jointed together) isn't behaving very well at all.
Picking it up and dropping makes the Crystal Bag add copies of base and symbols to itself, clip through the table and absorb anything in its path. This makes the process of setting up the Mana Crystal in Mana Crystal Room incredibly tedious, fragile and annoying. Reproducible on my machine with Full and Locked physics.

Problem in action: https://streamable.com/ua4w4