How could I set up a circuit that keeps track of strikes in a baseball game using D flip flops in Multisim?
While I'm not a Multisim  guy, I suggest that you haven't tied D0 to any thing. Try tieing D0 to a logic high.

Furthermore, I suspect that your description means that, the sequence of LEDs should look like

Start  Q0 off, Q1 off
Push   Q0 on, Q1 off
Push   Q0 off, Q1 on
Push   Q0 off, Q1 off
Push   Q0 on, Q1 off
Push   Q0 off, Q1 on
Push   Q0 off, Q1 off
etc.

If this is so, you need a second input - Start, to force the FFs to the starting position. This may not be true for Multisim, as the program may initialize FFs to 0, but you would need it in real life. Assuming that no Start is needed, 







simulate this circuit &ndash; Schematic created using CircuitLab

will do. Obviously, if a batter has one strike and gets a hit or a walk, you can push the button twice more to get back to the starting state.