I spent a moment with @CCP_Savior looking at this in an abyssal site that contains one of these extractors, and verified that having this problem depends on the specific site you’re in and the placement of the extractor on one of the rocks. There are a lot of sites and extractor placement combinations.
If you can submit an in-game bug report when this happens (press F12 and click Report Bug) the information in the bug report will help us identify in which site this is occurring, and that would be a huge step toward finding and fixing the problem.
Edit: I’ve been told that we did make a pass through all the sites before release to identify and fix collision problems with Triglavian Extractors, but it sounds like we’ve missed an instance of it. So, a bug report submitted inside the site would be a big help, if possible.