Just in case that you do not know this, all modern VAG exhaust sections are joined by using "jointing pieces" - they tend to be same diameter at both ends. All modern VAG replacement exhaust sections will be manufactured to be just a bit too long, basically to give the person sawing a duff section out a fighting chance of making a proper repair even if they misjudged where to cut the old part. So, I'd always consider that when replacing two pieces, that a bit of one or both needs cut out so that when the parts are aligned there is a very slight gap - that way the jointing piece can be fitted without it causing a misalignment in the pipework. Does any of that make any sense or explain why you are having problems?
One other question, have you been buying VAG parts or aftermarket copies? Also, for some clever reason, Seat do tend to change exhaust parts design during a production run, I had a
problem with my daughter's old 6K
Ibiza 1.4 8v, after giving local Seat dealer all the correct info, they ordered in the wrong rear box "oh, it must be the other one you need!" I'd rather think that the parts catalogue would have made that clear, the car was on its original exhaust.