When using Clip to DEVONthink in Safari I’m taken away from the current space, it switches to another space automatically. Everything else is ok, but I have to go back to the previous space manually. I’m quite sure this behaviour didn’t occur in previous versions, but can’t tell exactly when it started (but it started before the last update). This gets quite annoying when adding stuff…
Spaces are actually completely controlled by macOS, the updates of DEVONthink shouldn’t change this behaviour therefore. Did you change the Spaces settings lately or did you upgrade macOS?
I upgraded to mojave some time ago and also began to use TotalSpaces some months ago. Can’t tell when this started, but I’m quite sure I would have guessed it were related to mojave or Total Spaces if it occured around that time. Nothing wild, otherwise I would have asked weeks ago. Just wanted to check if this is perhaps a known issue. Shows one more time that my “rule” of only installing one app at a time would be helpful - if I followed it 
Just if this is of interest: the same behaviour occurs when syncing DTTG while a DEVONthink window is opened on the current space. Seems that for every database that is synced the space switches away again (if I previously switched back to a space with a DEVONthink window manually).