Yes, reverse polarity causes damage to polarized capacitors (super caps are polarized), this either causes outright failure or damage to capacitance and lifespan. There either can be visible or non-visible damage. I would not trust them if they did see reverse polarity.
For me, I was building my own capacitor sets and using Zener diodes even on the 3V versions to ensure balancing and no reverse voltage problems. I know many folks just use the supposedly matched pre-connected 5V pairs.
That said, I would never go on wire color alone. Are you sure the connection to the board is correct? This was a recent discussion with pictures https://ogrforum.com/...4#164588232434864614
It's possible a mistake was made, but also, the 9V style of super capacitor ofen did require reversal and someone got it wrong for a 3V.