Hello,
.
Yes, in many cases OMR sheets were rejected, state, CBSE students both will have same OMR sheets, even if there question paper varies. Rejection main reasons are,

• Marking twice from same blank
• using wrong markers
• Wrong roll number or Wrong bubbling of roll number

And many reasons you have, that's the reason separate time will be give  to fill  OMR just because it's a complex system.