I've been practicing for a while, but two days ago, I ran into a problem I'd never had before.
I'd been practicing for a while, but two days ago, I ran into a problem I'd never had before.
#2 is not wrong, but if you are still practicing I'd choose #1. I see no reason for a comma after 'ago'.
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#2 is not wrong, but if you are still practicing I'd choose #1.
I see no reason for a comma after 'ago'.