There are tons of examples where otherwise "harmless" Tamil words developed negative connotations in mallu.
വളി in Tamil means "air". Just air.
വെളി in Tamil means "outside"
Both are words, word roots in mallu also.
വളി came to mean stale air, stench (cf. വളിക്കുക), and by extension അധോവായു.
വെളി still means outside. However, in the euphemism "വെളിക്കു പോകുക" it has picked up a negative connotation.
Yes, I used examples that are "mostly harmless". There are other words that might be a bit "hairy", which clearly demonstrate that the original Tamil word was entirely neutral but the mallu cousin is totally shady.
The more interesting question is why could such negative connotations have developed? An indication of class structure wherein language of the upper class (Sanskrit) was considered more refined and positive than the language of the lower class (Prakrits and Mallu)?