When the scanner load project repositories (batch/project WS) it should not fail when receiving a 404 since it simply means this is a new project, and that autoprovisionning should happen (with default quality profile).
But it seems timeout and other errors are also ignored. The WS may take a while to respond for big projects, and it leads to analyzing the project with the default quality profile:
(default timeout is 60s)
Except if we are missing something here, only 404 and 200 should allow the analysis to continue.