At the early stages of the legislative process, every time this was brought up people kept saying, "it's fine, they've excluded non-commercial open source". Now it seems there are problems with what might count as "commercial".

But at this stage of the process, the EU legislators can't make arbitrary amendments. There are two versions of the text now - one proposed by the Parliament, and one by the Council - and the final text must be a compromise between those two. It can still be rejected by Parliament, but that would be rejecting it in whole (and they won't do that).