Double transactions

Today when I check my balance it showed a negative and when I went to the bank to enquire they told me it's transactions that were not banked by the places I used my card at but every time I use my card I make sure there are funds available so that I can transact. Now it looks as if I am expected to pay twice for the same transactions. what I know is when I swipe my card the funds goes from my available balance to balance"pending transactions " and whatever funds didn't get banked on the day I swiped my card those funds can be deducted from the funds that are in the balance side(pending transactions) not to be taken from my available balance again.