Desktop software ignores the middle names because that is not a standard gedcom field.
Sources in the bio are turned into wiki markup or html code (not sure which) that is a lot of work to cleanup.
Some wikitree specific fields are exported and get imported into your software.
Other last names get put into a given name field (in RootsMagic anyway).
When baptism/burial dates are used in lieu of birth/death dates you need to fix these.
Formatting in the bio (bold, italic, indent, etc) gets turned into code.
Children are usually not in chronological order.
If children are not linked to two parents you can get phantom spouses/parents (in RootsMagic).
There may be other issues ...