In certain cases, especially when recently build kinda close (with kinda close I mean around 20 meters, not 3 meters, the range used in Vis.Entities) and you use /up it sometimes grabs other buildings which are like 20 meters apart. I scrolled through the code myself a bit and couldn't see anything wrong with the Vis.Entities Distance or other functions so can't figure it out myself, thought the plugin maker himself would have a better chance to have a look at it.
It seems somewhere in the code a building block gets put into the list wrongfully or something causing the complete building to get upgraded and possibly causing a chain reaction.

Sorry for the delay in response as I've just recently adopted this plugin. Give me a few days to get around to doing my initial code cleanup and from there I'll start rewriting everything as it's quite difficult to pick up where someone else left off.

Hey there, I forgot completely about it, I managed to fix it myself, it was a bug in the raycasting function I noticed, I replaced the raycast with a different one which fixxed the error completely, I based the raycast on the one from R-RemoverTool.
This is the GetTargetBuildingBlock function I replaced it with:
https://pastebin.com/9kn6x0iw

hope this can help a bit.