Each time a reader clicks on your site, each of your ad spaces undergoes a competition in which hundreds of thousands of advertisers bid for the opportunity to show their ad in that space.
Advertisers want to advertise to people who are interested in their products, so their bids are based on a couple things:
1. The content of your site. Food blogs will get more food ads than other types of blogs, for example.
2. The specific reader's browsing history. If you've been car shopping online, you'll suddenly see lots of car ads everywhere you go. Your readers are seeing ads that are targeted to them, based on what they've been doing online.
It's totally possible that an advertiser might bid for - and win - every ad space on your page at once. This happens because they're willing to pay you the most money at that specific moment and for that specific reader. It's a good thing: you've just sold your ad space for the highest possible amount!
The only way to prevent this would be to sell your ad spaces at a lower cost, to a different advertiser who bid less for that space. However, having the same ad appear on multiple spaces is totally normal, and happens across the internet all the time, with all the most professional publishers.