I just generated a new coinomi wallet and it gave me two of the exact same words back to back in my 24 word recovery phrase.
As noted by other replies here, there's nothing wrong with having repeated words on the phrase. It's uncommon but not astronomically rare.
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
This problem is only during verification. You can skip it and restore the phrase again to check that it's correct. This is known issue on the desktop version that is fixed and ready to be deployed on our next update, we apologize for the inconvenience.