I ran in to the exact same issue. The extension is sadly not documented (https://github.com/dotnet/aspnetcore/issues/19098) but digging through the source it looks like intended behavior, but i cant find why swagger works.. The source code says "Proxy all requests" (https://github.com/dotnet/aspnetcore/blob/e2a857c8ccda4dcfac3381a166faaf3542d85c62/src/Middleware/Spa/SpaServices.Extensions/src/Proxying/SpaProxyingExtensions.cs#L73)
I have also tried downgrading the extension in my project to get it to work since this issue seemed relevant https://github.com/dotnet/aspnetcore/issues/52308 but there was no change.
If you find out how to proxy all requests except the ones matching swagger and controllers I would be very glad.