Two-Stage Common Emitter Amplifier Is Clipping Unexpectedly
I'm unable to explain the behavior of the first stage



Single resistor biasing of a base like you have done is never very precise and relies on the hFE of the transistor for setting the quiescent DC operating point (bad). Use a potential divider bias with lower values like tens of kohm.
Relying on emitter resistor bypass capacitors for increasing gain inevitably introduces bad distortion. Do you see this technique ever used in any op-amp?


Result is drift and distortion.