That is 100% a bad charge pump IC4 - TC1044SCPA). Easy check is to remove IC4 (I socket all my ICs and transistors for this reason) and the pedal will then only be operating on your 9V supply and the square-wave oscillation will be gone.
Rationale: There are a few charge pumps which all have basically the same intent and pinout (TC1044, ICL7660, lT1054, etc.). Some versions are suitable for audio use and some are not. Also, some nefarious sellers from overseas will mark one of the ICs as the preferable type and it is actually the cheaper to make, non-audio version (eBay, Amazon).
They use an internal oscillator and capacitors to create a switching power supply, which doubles (or more, depending on the circuit) the voltage. The frequency to which they 'switch' is from 25kHz to 30Khz, just above audio frequencies. However, when they are not properly constructed they do not filter out the even-order sub-harmonics of the square-wave oscillator. What we are hearing on the clip you provided, is a 50Hz square wave sub harmonic.
I use ICL7660CPAZ and buy 10 at a time from Mouser (reliable source) for around $27 (2.70 each) delivered and have had no harmonic problems.
I've built two of the Lead Solder ODs and the only problem I have had has been since wave internal oscillations from too much gain, combined with the tone controls maxed and have posted a mod on this forum which prevents that by using lower values for R10 (510K) and C8 (200pF).
Hope this helps.