Are you sure that the other address that received bitcoin wasn't simply the change from the first transaction and not actually your bitcoins? Depending on the website you received funds from, they likely sent you your bitcoins and the change from the transaction went back to their own address.
I don't know too much about the bitcoin system. All I see is that the website sent the full amount. I received most of it to my correct wallet, but there is another chunk to an address I have never seen or have access to. The site is trying to research the other wallet address. Other than that I'm bewildered.
If you didn't, this isn't Electrum's problem.