PWM logic level issue
Which is the Pin you are worried about? Here is how you can go about finding the root cause. 


Make sure the power supply is stable. Measure the 3 V supply 
Make sure the GPIO pin is disconnected electrically from all the components. Remove series component if any or lift the MOSFET if it is connected.
Drive a test frequency signal and monitor waveform (you have done it for 250 Hz)
Enable PWM and drive it again with lower frequency
Increase the frequency to higher value (actual value)
PWM is a Digital output toggled at higher frequency. Hence, the Singal level on oscilloscope MUST reach 3.3V or the MCU VDD how much ever it is
Please post complete schematics section and if the GPIO outmode is able to drive the signal to complete logic 1 and logic zero,there is no way a healthy MCU would fail to create the same logic 1 and logic 0 signal for PWM. 
I suspect that the pin is getting loaded but we will see when you share the complete schematics related to PWM pin part 
Pleas verify once that the probes are with high impedance DC coupling settings