Why do 3.5 inch floppy disks have sometimes three and others four holes on the backside? What's the difference, what do this holes indicate and what are these used for?
The upper two (or one) notches at the sides, are to grab and clamp the disk against ejection - an addition Sony made to the 3.5 design on request by Apple, which had that already patented for the twiggy drive.
The lower two round holes are for precision alignment used during production to hold it exact in place. They may as well be used by some of the higher capacity drives, like LS-120/Superdisk.
The diskette housing is pressed down onto alignment pins that engage two of those holes, which keeps the motor axis at the right position that the diskette is free to rotate in its housing (doesn't rub the sides) and the sliding door on the diskette engages the retraction finger.
A third hole is for the write-protect tab, while a fourth is indicative of high data density (a superfloppy holds 1.4 Mbytes, while 'standard' doublesided hold 720k to 800k bytes).