H-bridge problems

Has anybody ran into this problem:

I have an H-bridge as shown in the attachment. when I go to a logic 1 on the driving fet the whple port goes to 0. If I one drive one have of the h-bridge then it does not effet my micro. I think it's due to shot-through on the h-bridge

you mean mcu reboots when this thing is turned on or only
one port is affected? does this happen when you use h-bridge without load?
are they both (mcu and h-bridge) powered from same source?
is the voltage for mcu regulated? do you have capacitors?
does this half bridge have internal diodes?

Well, for starters, that is NOT the correct pinout for an IRF7307.
1 S1 8 D1
2 G1 7 D1
3 S2 6 D2
4 G2 5 D2

Turning on both transistors at the same time is a problem inherent to all H-bridges. There are many good solutions. Perhaps the simplest is to control the N and P with separate inputs so the controller can insert a delay between turning one off and turning the other one on.

You do need diodes to protect the transistors. When the power is switched off the inductance of the motor makes a high voltage spike if there is no diode to route the current away.