The cljs.core/implements? checks whether a protocol is implemented via a property on the tested object. When implementing the protocol this property will be set to true.
This works fine under :none but :advanced may rename this to something like x.A. If you now try to check (implements? TheProtocol js/window) for example it may (or may not) report a false positive. For larger projects the likelyhood of creating a false positives goes way up since window contains all the variables created by the advanced compiled js.
The attached patch changes the patch the emitted code to check x.protocol$check$TheProtocol$ === true which reduces the chance of a false positive by a lot. We might chose another sentinel value instead to reduce the chance some more, this seems good enough though.