Leandra Issues with instant payments can have a multitude of different causes. As SCT Inst is fundamentally an asynchronous scheme where messages are exchanged between banks through a mediator (clearing house), there are many different systems involved when sending such an instant payment. Depending on which banks are communicating, different mediators are used. That's why it's not impossible for instant payments between bunq and Rabobank to work fine, while instant payments between bunq and ABN Amro to be broken. That doesn't mean that there's any issue at bunq itself (but of course we cannot fully rule it out without any confirmation from them).
As for how often something like this happens: if we look at a European scale, then probably all the time. SCT Inst is inherently fragile because of its complexity and the many different stakeholders cooperating. Usually this is not a big problem, though, because there's always the fallback solution of regular SEPA bank transfers available. These take a while (1-2 business days) but as they're the base standard and a lot slower, they're also a lot more reliable.
Alex In case of errors with top-ups, the payment gets automatically returned. That's probably not related to the instant payment issue that is the topic of this thread, however.