if the anon set is low on that coordinator and blacklisted UTXO's are allowed into the coinjoin could that potentially flag my non-blacklisted coins as blacklisted?
No one can provide a completely satisfactory answer to this question. Generally, if you use services that discriminate against users based on flawed blockchain analysis results, you could be blacklisted even if you haven't used coinjoin. This could happen because the previous owner of your coins was flagged by their systems, and as a result, you could be flagged too. If I remember correctly, there have been instances where Wasabi coinjoins were flagged as "suspicious" activity by popular centralized exchanges.