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Here are two instances I just quickly found:

I definitely also remember there being more examples, since I specifically researched this question of potential payout fees a lot (around the beginning of this year).

I fully understand that the TOS have always given you the potential to apply any additional fees before making a payout, I have read them entirely. My point is that you have communicated something else, are now going against that and officially introducing new fees (perfectly okay) but also applying them retroactively (not okay).

Let's have an example. You are currently not charging a fixed hosting fee, but have instead implemented your "Open revenue sharing" model. You still have to pay hosting fees yourself, I think everybody knows that. Your TOS give you the option to deduct these fees from every payout but you have communicated that you don't. Based on this information people are deciding on a revenue share. Now, you could come along and replace the open revenue sharing model with a fixed percentage fee, but then saying "Well, we've always had to pay hosting fees, so now you're going to have to retroactively pay them as well" would again be unacceptable (even though technically in accordance with your TOS). It's a communication and trust issue.

As I've also tried to stress before, (at least to me) this is absolutely not about the amount of extra fees I've had to pay. As you said yourself, it was not that much in the grand scheme of things, which then again makes me understand even less why you didn't decide to just waive them as well instead of setting the precedent of introducing new fees against what was communicated and retroactively applying them.

Quick sidenote, since I just noticed it: The link for "Read more about PayPal fees" here is broken.