Generally, it's way too easy to reverse a SEPA payment for a customer (up to 8 weeks if I recall after purchase). It led to some, admittedly rare, cases where we can issue a refund to a customer and then they'll reverse the payment as well. So we ended up with negative revenue to the same amount of what we charged, which can be up to 190 EUR. So we'd actually refund 190 EUR and then lose another 190 EUR + Stripe chargeback fees on top. Ouch. There was little or nothing we could do about it apart from begging the customer to transfer the money back to us...
On top of that, there were chargeback fees even if the bank, rather than the customer, reversed the charge. This happens not too infrequently (IIRC around 5% of transactions). If this was a credit card transaction, the bank would simply decline the charge. With SEPA it's not as simple... The charge gets through, supposedly, and then bounces with a chargeback fee...
Another thing I should mention is the async nature of the whole thing. Unlike cards that get authorized/declined instantly, we're talking days or weeks with SEPA. For a monthly subscription, this eats into the first month easily.
Again, we're talking about private individuals here (B2C), typically students in our cases, and as I mentioned predominately from Germany, so YMMV a lot with other customer types or countries.
[0] https://stripe.com/docs/sources/sepa-debit#create-source
Would you share more details about this, if you can?