Two things -
1. The location of the timing cover is determined by the front seal. The nose of the crank should be centered in the seal to avoid leakage later. The bottom of the block may or may not line up perfectly. Once you are happy with the location of the seal, use some silicone when you install the pan to bridge the gap.
2. If the dots on your cam were off (both at top), you would just turn the crank one complete revolution and they would line up... since the cam turns at half the rate of the crank. Both dots at the top would indicate that the #1 cylinder was at TDC on the exhaust stroke, not the compression stroke...
As long as they were referenced properly (both on top, or pointing together, you are good to go. Sorry to hear you already took the timing set off to correct. No worries though.