Update 7 is now available and the bugs you found have been fixed. You'll be pleased to know that it's now possible to grapple replicons and other objects into and inside the refinery. This proved to take far more effort than expected. Bugs were cropping up everywhere once grapples were still allowed to be connected to objects being refined. It was worth the effort though and allows for lots of interesting new gameplay possibilities both now and in the future.
Let me know if you run into any problems. Everything should be fine though.