This is a known issue but I don't really have a solution for it that won't impact performance.
This issue is fairly rare and once you know about it can be easily avoided by either clearing out trees before placing blueprints that will take a long time to build or placing blueprints that build reasonably quickly.
I'l look into it once again but as mentioned before trying to resolve this may be fairly performance intense and may not be worth the performance penalty for this fairly rare case.