Definitely just a misuse of the term. "Poison pill" doesn't just mean a terrible provision of legislation - it's possible for legislation to be terrible while conceived entirely in good faith. In this case it's bad legislation due to EU legislators not understanding open source.

A "poison pill" provision or amendment is an element deliberately added to turn people who otherwise would have supported the legislation against it. The person proposing the poison pill is acting it in bad faith - they have no expectation of it passing, they might not even support the idea themselves - the only reason it's added is to make the original legislation's supporters drop their support, killing said legislation.

I don't think anyone is seriously proposing that the EU is deliberately hamstringing open source in order to kill their own cyber-security act. They've just written a bad piece of legislation.