Is there a problem if I filed separately my Tax Returns because I have 2 SIN, (one SIN as temporary resident and one SIN as a Permanent Resident? How do I file this?

I have filed my 2019 Tax returns via Turbo Tax, I have 2 SINs when I filed and filed separately, and receive a refund for 2 separate Tax Returns used, and now I received a Notice of Reassessment saying I owe CRA, is this the reason? The reason CRA gave is not very clear to me, so I'm suspecting this one. Please I need your insight about this, before I go to my tax accountant. Thanks all...