Mud cakes are a VERY liquid cake batter. So it may not have been that. Did you cool down your liquid ingredients to room temp before adding to your dry ones? Did you mix thoroughly before placing in your cake pan? Did you melt all the chocolate and butter until perfectly smooth?
If you did everything right, and the cake is not tapered from top to bottom (on its sides) then I would say it is within normal limits. You can fill any mild dimpling with ganache as you 'crumb coat'. I never bake my mud cakes in bare pans, always line them with baking paper as they need to bake slowly at a low temperature and if you don't line them it can cause the sides to brown and dry out too much.