It seems that some areas connected well, and some did not (on both CSG v1 and v2)
In v1, such faces are created when a part is not precisely placed in relation to the other part (partially due to Floating Point error).
It usually helps if you drag the [separated] part with your mouse on the other part, so their surfaces get sticked to each other. That should create a fine connection that will allow a Union to be unified properly. If that won’t work, fixing a part’s position should do the job.
You may try these techniques and maybe the faces will disapear, however I can’t say for sure since - after all - it’s a different system.