Hi Badal,
It is impossible for the two output transistors of the LM3524 to be in phase, as far as I know.
I suspect that your scope triggering is set to alternate trigger.
If you can't set your scope to trigger off just one channel, you should have an external trigger input.
Connect one of the output transistor emitters to the external trigger input of your scope and select external trigger.
Alternatively you can set your scope to chop if the signal frequency is low enough.
spec