As skrotil has kindly replied above, this is not a bug, but a part of the UFO delegation system that was re-introduced in milestone 6, wherein doing more than 2 crash site missions of a single UFO type (for example doing your 3rd Scout UFO mission), will cost operation point)
I suggest posting a feedback thread on Xenonauts-2 General Discussion - Goldhawk Interactive, as we make sure to read through community feedback and changes are more likely to be implemented if that's what the playerbase wants (we do a big round up of feedback and suggestions every few months and then decide on which things to implement or add to our to-do list)