Unless someone can produce toml files that reproduces this it will be difficult to tell what is going on. I can at least verify that basic examples work as expected:
$ pkg st
Status `/tmp/tmp.YQdQZVnahc/Project.toml`
[a93c6f00] DataFrames v0.21.6
[7876af07] Example v0.5.1
$ pkg up DataFrames
Updating `/tmp/tmp.YQdQZVnahc/Project.toml`
[a93c6f00] ↑ DataFrames v0.21.6 ⇒ v0.21.7
Updating `/tmp/tmp.YQdQZVnahc/Manifest.toml`
[a93c6f00] ↑ DataFrames v0.21.6 ⇒ v0.21.7
$ pkg up
Updating `/tmp/tmp.YQdQZVnahc/Project.toml`
[7876af07] ↑ Example v0.5.1 ⇒ v0.5.3
Updating `/tmp/tmp.YQdQZVnahc/Manifest.toml`
[7876af07] ↑ Example v0.5.1 ⇒ v0.5.3