I told people to avoid using certain flags as emoji etc for religious reasons (e.g. UK, with its saints' crosses, and Japan, whose sun disc, though not officially religious, is linked in Shinto to the sun goddess). But I'm doubtful now if this is really haram. Is it ? If not how to repair this ?

Ustadh AbdulAziz al-Haqqan

Yes, it is better to stay away from using such flags. As for the people you told, there is no harm in letting them know that staying away from these is what is better.