Why would btfss fail sometimes on PIC12f1822
The BTFSS instruction isn't just going to fail randomly.  You're not going to find what is wrong with your circuit or code until you stop trying to blame the PIC.  There is something wrong with your setup.

First I would simplify the code.  Going thru INDF registers to access ports adds another layer of stuff to go wrong.  The comments (sparse as they are) say that INDF0 is supposed to point to PORTA and INDF1 to LATA, but I don't know that nor do I see any evidence this is actually the case.  It's also not clear what CS_INPUT is supposed to be, and why it is relevant to your test anyway.

If you are having a problem reading a input pin, write a loop that just reads the pin and mirrors it to another pin.  That will probably work fine.  Then keep expanding that step by step until some incremental step exhibits the symptom.  Now you have a much better idea what might be wrong.  And no, it's not going to be the BTFSS instruction failing.

It would be good to look at the Vdd pin at the same time you see the glitches.  Maybe the 5V supply isn't as clean as you think.  Maybe something else is causing occasional glitches on the supply or the other lines.