Removing a block from a template in the building editor will visually remove the block, but the template appears to think there is still a block there. If you try to add a block to an area you’ve removed things, it acts as though there are still things there.
Saving the template and adding it elsewhere doesn’t help. Closing the game and reopening doesn’t help (as well as being super inconvenient anyway). This issue has persisted for the last few patches and I’m hoping it gets fixed soon as it makes building anything interesting pretty impossible.