I can't name any specific situations, but it will generally come down to the fact that your project is different from whatever the script writer was anticipating.
For instance: import statements vs. require expressions - these need to be handled with different AST matchers. Import statements themselves have 3 different varieties of specifiers (default, named, "all") which must be accounted for. A require expression may or may not involve destructuring, it may or may not use const or let over var (each of which need to be handled explicitly, etc.)
As far as failure mode: scripts generally just won't match or work, or they might replace all of your consts with vars, etc - they can be very codebase specific depending on the complexity of the script.
For instance: import statements vs. require expressions - these need to be handled with different AST matchers. Import statements themselves have 3 different varieties of specifiers (default, named, "all") which must be accounted for. A require expression may or may not involve destructuring, it may or may not use const or let over var (each of which need to be handled explicitly, etc.)
As far as failure mode: scripts generally just won't match or work, or they might replace all of your consts with vars, etc - they can be very codebase specific depending on the complexity of the script.