Basis my experience, top 3 challenges are -
a. Alignment of tech team with why? - tech easily understands the what to do and they obviously know how to do. but unless why can be synced, it is always back and forth
b. sometimes in agile development, the changes has to be reworked which cause lot of resistance from tech team and that sometimes shows in the output.
c. estimations - have not seen this come true even after multiple releases. tech team generally considers the actual coding effort but always forgets the bug fixing or any other efforts.