Thanks for the report. Is this similar to issue10375 ? One option would be to use -p to stop transforming print related code if you don't want to transform any print statement.
$ cat /tmp/foo.py
print (1)
$ 2to3 /tmp/foo.py
[snip]
--- /tmp/foo.py (original)
+++ /tmp/foo.py (refactored)
@@ -1 +1 @@
-print (1)
+print((1))
$ 2to3 -p /tmp/foo.py
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: No files need to be modified.