Well, TAP is certainly on my personal No-Fly-List, because of their very bad behaviour. However, in this case they were right.
I have flow several times during the last year but never in transit. our fault was looking at departure and arrival and omitting the transit airport.
Was that a package holiday or did you book the flights by yourself? I guess the latter, because you were asking for a chargeback.
Why am I raising the question on package holiday - if the package holiday operator changed the flights and put you on TAP (with a third-country transit), then you may have a case against the package holiday operator.