I thought that was weird as I was under the impression that they're meant to be randomly generated and the odds of that happening must be astronomical.
There are no rules against the same word appearing twice in a seed phrase, and nothing in the BIP39 code to stop it from happening. On average, about one in every eight 24 word seed phrases generated will have a duplicate word. It's a bit more uncommon for them to be next to each other, but certainly not astronomical nor impossible.
Then when it asks me to confirm my seed on the next page I get all the way to the last three and when I click on the first same word both of them disappear when I click one of them but only one is logged which then leaves me with the last word, but when I click that it won't let me proceed, so I'm guessing this is an error. I can skip the step but if I've got a faulty seed then obviously that's very bad, so does anyone know whats gone wrong here???
This does sound like an error on Coinomi's part. If you are unable to properly verify the seed phrase due to the duplicate word, then I would scrap the whole thing and start again. Do not proceed with a seed phrase you cannot verify.