Highpass filter square wave
That's perfectly normal and expected. You are removing harmonics and as a result you change the time domain wave form. There is no guarantee or expectations that the maximum amplitude will be maintained.
In fact, a square wave has the lowest possible Crest factor (ratio of peak to RMS) and ANY change will increase the Crest factor. In order to not clip you need to remove a substantial amount of power (which your lowpass probably does).