Looks to me like it was poorly aligned in the chain tool - either because the chain tool is crappy (there is a wide variety in tool quality, and "multitool" chain tools can be particularly bad), you were working in an awkward position (with the chain trying to fight its way out of the chain tool while setting the pin), or your chain wasn't layed in the "primary" position on the chain tool - the position furthest from the crank of the tool, up against the main anvil, if that makes sense. You can place the chain in the tool in a position closer to the crank of the tool, but that position is for loosening tight chains, not pressing pins in or out of the chain.

Chain removal: http://www.parktool.com/repair/readhowto.asp?id=25
Tight link repair: http://www.parktool.com/repair/readhowto.asp?id=53

-Sam