Can be confirmed by running the synthtests (B button) in the sndtest.lua example project. Instead of removing the lowpass filter effect at the end, the removeEffect operation is a no-op and it keeps layering the lowpass effect. Works properly in 1.12.3.
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Well caught! I've added a fix for the next release.
To be totally pedantic here: The bug was due to a big under-the-hood change in 1.13 where I updated all of the Lua code to use the same LuaUDObject wrappers that the C API uses so that we can pass objects back and forth. That is, pd->lua->getArgObject() should now give you the correct C API object for the given Lua type. I spent a very tedious afternoon auditing the code to make sure I was using it consistently, but somehow missed this one. 
That's fixed now and I'll take another pass to see if I made the same error anywhere else.
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