The problem occurs to me also when I want to "deepen" a shallow clone of
MediaWiki via https://

 git clone --depth 1 https://gerrit.wikimedia.org/r/p/mediawiki/core.git
 git pull --depth=99999

fatal: git fetch-pack: expected shallow list.

Perhaps it helps someone to find the reason.

UPDATE:

This however works

 git clone --depth=2 https://gerrit.wikimedia.org/r/p/mediawiki/core.git
 git fetch --depth=5


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