Does this mean that Filter::Util::Call confilcts with the builtin eval function?

No, its merely a listed caveat/limitation wishful thinking? bad memory? what?

Source filters in eval/require

Its from reading perlmonks that I know filter doesn't work in eval from this tutorial Including files

update: finally paged through this search ?node_id=3989;HIT=eval%20filter

Source filters in eval/require

source filters in eval

So there you have it :) it should be documented or something ... I don't know :)