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Both EU and Non EU seperated for very long time ( not divorced )

NON EU applied Settled Status but without EU Sponsor Residency Proof but he mentioned in the cover letter that he still has JOINT BANK ACCOUNT with his EX even though they are not living together for very long time.

CaseWorker called and asked for that Bank Statement which he mentioned in the cover letter

NON EU send that JOINT BANK STATEMENT and again wrote to the Caseworker " I'm separated from my ex wife for long time " i am sending this BANK STATEMENT because you asked for it even after knowing we are seperated

NON EU granted Settled Status

EU citizen Apply Settled status after few month but with completely different Proof of address so now their proof of residency don't match.

IS IT CONSIDERED DECEPTION in the EYES of HOME OFFICE ?

It doesn’t seem like it to the best of my knowledge. You can still operate a joint account after a divorce and that is substantial proof, and it shouldn’t be a problem if only one party decides to rely on it as proof of such relationship, as you did state vehemently when sending it that you both are no longer together. I don’t think her application should even be tied to yours or any confusion regarding deception. Home Office won’t normally operate like that, as it is on a case to case basis and the person who will probably look at hers, won’t have been the same person who looked at yours.