On top of my head, there's the Deino line, which has also been mentioned by others. I pronounce them so that the German words Ein, Zwei and Drei are audible. I don't think that is correct from an English perspective, but I prefer it that way.
I don't know how specifically you pronounce them, but officially they are indeed pronounced in a way that Ein, Zwei, and Drei are audible even if those are German, in part most likely because those specific words were intentionally integrated into their names relative to the number of heads they possess (even if two of Hydreigon's heads are fake). Going off the anime, the official pronunciations for them are such that Deino is pronounced dino (thus the "ein" in German is audible), Zweilous is zwai-luhs, and Hydreigon is hy-dry-guhn. So the fact that they have the German words Ein, Zwei, and Drei in them is very much acknowledged in their official pronunciations and it seems that is indeed the proper way they were intended to be pronounced, even from an English perspective.
Unsure if this is incorrect, but I say Arceus with a soft C. This is because it was pronounced that way in House:
Arceus is a really weird case, because even though the official English pronunciation uses a hard C, the Japanese name アルセウス is transliterated to Aruseusu, and you can see based on the transliteration that it would imply it is "Arceus" with a soft C.
In fact, before the Arceus movie came out which is the first time the hard C Arceus pronunciation was officially used, many of my friends back in elementary school (back when Gen 4 was still going on) always pronounced Arceus with a soft C: I myself used the soft C Arceus pronunciation. It really feels like the more intuitive (and imo more natural) pronunciation for Arceus in that sense. So the hard C official Arceus pronunciation definitely came off a bit odd to me (and to many others too) when it was officially used in the movie and now with PLA trailers. Considering the Japanese name is technically the same as the English one I'm not sure what led the localization staff to use the hard C instead.