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The fixers are supposed to be executed on Python 2 files where apply was a builtin and was shadowed. So from the context of the fixer it tries to make the modification and it cannot distinguish that it's a builtin or user-defined call. In Python 3 the apply function can be defined by the user and 2to3 fixer doesn't make sense to be executed on Python 3 files. filter is another example where the call is transformed into a list comprehension by 2to3 but by the issue it shouldn't be done because filter is a user-defined function though it's a builtin in Python 2.
def filter(func, iterable):
 pass
filter(lambda x: x % 2 == 0, range(10))
RefactoringTool: Refactored /tmp/foo.py
--- /tmp/foo.py	(original)
+++ /tmp/foo.py	(refactored)
@@ -1,4 +1,4 @@
 def filter(func, iterable):
 pass
-filter(lambda x: x % 2 == 0, range(10))
+[x for x in range(10) if x % 2 == 0]