Can my CoE be denied if a company didn’t withold the right amount of taxes from my salary during a previous stay in Japan?

As I wait for my CoE I have entered an unavoidable state of paranoia and I'm going through every possible thing that I might have done wrong and can come bite me in the ass.

In this endeavour a realised that the modeling agency I did a couple of jobs for only withled ~10% resident tax instead of the ~20% resident tax that was in order (as I was on a Working Holiday).
I've calculated that, in total, they should have witheld around 5000 yen more than they did.

Additionally, I completely forgot to notify my keiyakusho that I was leaving Japan. I presume this tax discrepancy could have been settled then and there if I had done the proper procedure.
My total income while in Japan was 80,000 yen, as I lived off of savings, so I didn't need to file a tax return or anything like that though.

How can I go about paying this?
Would they deny my CoE over this?

by No-Return9278

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