What annoyed me so far:
-Crashing with the buggy into things and damaging both (even at super low speeds!). Need to drive super careful

-Driving against a tree and coming full stop.
-Hacking away little fallen trees and stuff in big ore fields. Annoying!
-Pulling along an electricity line with poles, but not wanting to have gaps in coverage between them, which means playing each of them individually, rather than click&hold-drag.
-Having to manually sort my inventory over and over. Stack-all button would be so awesome!
-Navigating through a maze of pipes.