At the bottom of the page for this release it states:-
"In PAL, because of the considerable drop in quality on CGI shots, all of the shots including visual-effects in the episode "Sky Full of Stars" (about a quarter of the episode) are stretched sideways to fill the 1.78:1 format without too much loss in quality. There are also one or two shots in later seasons which use this effect to achieve the 1.78:1 without losing important parts of the image. "Sky Full of Stars" is all properly framed on the R1.
(Thanks to Cemetery_Mink for this info)"
This is correct for the original PAL R2 box sets (mine was bought in the UK), however Warners (UK) would send a free replacement disc (correctly formatted) upon request, later versions did not have this formatting issue.
Some of the later series' box sets had issues with a the odd disc, and again Warners would send replacement discs - e.g. in one episode, of the later series, the opening sequence in the broadcast version was "different" to normal, but when the dvd was made they just copied the normal opening sequence - Warners sent out replacement discs with the correct "variant" opening sequence.