I think they forgot to subtract my $5 coupon from the total when I paid.
I don't think they took off the $5 discount from the total when I paid with my credit card.
この場合、次のような言い方ができますよ。
ーI think they forgot to subtract my $5 coupon from the total when I paid.
「(店の人が)支払った合計から5ドルのクーポン分を引くのを忘れたようです」
to subtract my $5 coupon from the total で「合計から5ドルのクーポン分を引く」
ーI don't think they took off the $5 discount from the total when I paid with my credit card.
「クレジットカードで支払ったとき、(店の人が)合計から5ドルの割引を引かなかったようです」
to take off the $5 discount from the total で「合計から5ドルの割引分を引く」
ご参考まで!