What kind of file was it? Are you able to upload other files to that site?
Sometimes there are browser issues during the upload process that cause temporary issues. Please try uploading your file again, in a new browser session.
More specifically, I believe the upload_size app.yml setting is given to nginx as client_max_body_size, which is the same parameter provided in the two site settings descriptions:
Max image size KB
The maximum image upload size. This must be configured in nginx (client_max_body_size) / apache or proxy as well. Images larger than this and smaller than client_max_body_size will be resized to fit on upload.
Max attachment size KB
The maximum attachment files upload size. This must be configured in nginx (client_max_body_size) / apache or proxy as well.