If you're encountering some oddities in the API, here's a list of resolutions to some of the problems you may be experiencing.
404 error for an existing repository
Typically, we send a 404 error when your client isn't properly authenticated. You might expect to see a 403 Forbidden in these cases. However, since we don't want to provide any information about private repositories, the API returns a 404 error instead.
To troubleshoot, ensure you're authenticating correctly, your OAuth access token has the required scopes, and third-party application restrictions are not blocking access.
Not all results returned
Most API calls accessing a list of resources (e.g., users, issues, etc.) support pagination. If you're making requests and receiving an incomplete set of results, you're probably only seeing the first page. You'll need to request the remaining pages in order to get more results.
It's important to not try and guess the format of the pagination URL. Not every API call uses the same structure. Instead, extract the pagination information from the Link Header, which is sent with every request.