Those two flags have the same colour combination, but the green and orange are backwards.
Both flags have the same colours, but they're in a different order on each flag.
ーThose two flags have the same colour combination, but the green and orange are backwards.
「この2つの国旗は同じ配色だけど、緑と橙が逆です」
colour combination で「配色」
backwards で「逆の」
ーBoth flags have the same colours in them, but they're in a different order on each flag.
「どちらの国旗も同じ色だけど、色の順番が異なります」
in a different order で「異なる順番に・順序で」
ご参考まで!