I was using the original SNTD mod, and then switched to this one due to the crashing issue.
When I delete tubes (both in lab and on the normal world), the digits entities remain deployed and prevent anything from being built upon them.
Hm. Yeah, I've experienced that too. The original mod keeps a table of nixies that it uses to update from. For some reason the table get off, which is what caused the crash. I bypassed the crash, but the table is still off. I've been meaning to add code to recreate the table, and regenerate the digits.
Ok, I just uploaded a new version which adds some code to rebuild all nixie tables and entities every time configuration changes, or a mod is added/removed/updated. This should fix the hanging digits.