perl -0pe 's/pattern1|pattern2/$1/gs'; apparently the "or" operator doesn't work as expected here.
The | alternation operator has pretty low precedence, so it kind of depends on what your expectations are :-) A common trap is to write something like /^foo|bar$/ and expect that to match only "foo" or "bar", when in fact it is matching ^foo or bar$ - the correct way to express that would have been /^(foo|bar)$/ or /^(?:foo|bar)$/.
Based on your $1 in the replacement, I suspect you were doing something like s/f(o)o|b(a)r/$1/g and expecting the string "bar" to be turned into "a"? In that case, you need the "branch reset" pattern (?|...) (perlre): s/(?|f(o)o|b(a)r)/$1/g will replace "foo" with "o" and "bar" with "a".