The gallery leaves the cover image out on purpose. Your cover is already the large image at the top of the project page, and showing it again as the first item of the gallery would print it twice, so it is removed from the gallery list by matching its file.
Nothing has been deleted and nothing failed to upload. The cover is on the page, above everything else.
The count runs one behind the builder
Because the cover is missing from the gallery only, the numbering shifts. What the project editor calls your second image is the gallery's first, and the 1 of 12 counter in the full-screen viewer is counting eleven other images plus itself, not twelve including the cover.
This matters when you are describing an image to someone: say what is in it rather than which number it is, because the two of you may be counting from different places.
There is no setting that puts it back
Nothing in the builder controls this. The rule is fixed for every project, so a cover cannot be added to the gallery and an ordinary image cannot be pushed above it.
A project with no cover shows everything
If no cover has been set, there is nothing to remove, and the gallery holds every image, video and embed in the order you arranged them. That is why some projects appear to include their first image in the gallery and others do not.
If the cover is missing from the top of the page too
That is a different problem. It usually means the cover was never set on the published version, or the version being shown is an older one. Open the project in the builder, confirm the cover, and publish again.