> Is it common that developers still have issues with git after using it professionally for a couple of years?

As someone who has worked on developer tooling, including building a custom git client at a former job - yes.

Most people learn a few specific workflows not conceptually how things work under the hood.

Visual editors like GitKraken, Submlime Merge, Sourcetree, etc, have made this much better but there's still a big gap.