Ok I've only read the first manga but I did pick up on some differences between it and the anime from viewing the pilot yesterday:
*In the manga the organization that Cerishe and Ryohou belong to is
called the HOLY this is changed in the anime to the HOLD(and yes I did
check the manga before posting this and it is spelled out that it is
the HOLY and not the HOLD in the manga)
*Ryohou is introduced before Cerishe in the manga(actually they're introduced together)but in the anime we first meet Cerishe alone
*Kanami is pretty much the same in the anime as in the manga except
she seems to be a bit younger(my impression from the manga was
that she was at least 16 but from the anime she doesn't appear to be
more than around 13)
*Ryohou's powers appear to be different
*Kazuma is referred to as The Treasoner in the manga but he doesn't
appear to have acquired the nickname yet in the anime
*There is no older person referred to as "Grandpa" by Kanami in the
manga
*In the manga Kazuma states that Kanami was born on the mainland and
abandoned later on.