a fertilised egg might split days later and become two or more people. Where and when did the extra souls come from?
God creates every soul from nothing (creatio ex nihilo). Being directly created by God the nature of the soul is perfect and cannot be undone that's why the soul is immortal.
By revelation and respect for the unknown it's assumed this creation occurs at the moment of conception. If a fertilised egg splits we can assume the other soul is created at the moment of this division.
Most zygotes fail before implantation - where did all those souls go and why?
We don't know if it failed because God chose to not give it a soul. But if it was gifted with a soul, this soul goes to a Limbo. Because the final destiny of the soul is to be eternally united to a human body, but this destiny will be only fulfilled after the resurrection in the Last Judgment.
Sometimes two fertilised eggs will fuse creating a chimera. The person will develop normally. How many souls do they have? etc etc etc.
Every human have only one spiritual immortal soul.
God is not limited by time. He knows in advance that the egg would fuse or split, etc.