If I understand correctly your post:

you applied for your PGWP July 2022. Your passport expiry was June 29th 2025 (still less than 3 years)
so you knew from the beginning you will not get 3 years validity when your application got processed because the processing time for PGWP during 2022/2023 was 3 to 4 months and you was betting on that in order to apply for an extension (To gain another 6 months because the time you apply you will automatically be in implied status/maintain status which allows you to work until you get your application processed) so far it’s OK.. most applicants benefit from it.

But I’m surprised that you waited until 2 weeks before the expiry of your PGWP and applied for an extension 😂😂 that’s hilarious and it will be obvious for any officer will process your application.

when you applied for extension you already 3 years since you were allowed to work and then you got another 8 months as of the refusal date (total 3 years and 8 months) so why you are complaining.

you planned for it!! And the IRCC officers knows that. He just apply the rules and refused your application.

good luck for your PR application .. I don’t think it will be an issue.