Hi,
some thoughts:
* you say "SMPS", it means SwitchModePowerSupply. I see no "switch mode", nor a "power supply".
* in your circuit I see no inputs and no outputs. Where are the loops, what should we look for?
* if the simulation differes (outside tolerance) from the vero-board, then maybe you don´t have a suitable GND concept (like star point) on your Vero-design.
* my saying is: "A circuit without capacitors is no reliably working circuit". In my eyes an analog circuit needs power supply decoupling capacitors, filters, loop stabilisation...
* you say "is showing some negative voltages". Withou giving values and timing, or scope picture. Do you expect us to guess?
* what does "+ve" mean?
* what does "to trigger some circuit" mean?
* "reference voltage 1.24V is not showing on non-inverting pins". The 1.24V are not directly connected to the pins. There are resistors. And for resistors it´s quite usual that there is voltage across them (else they would be useless). Anyways: I don´t understand why you are worried. Without saying what you expect and what you see instead ... a discussion is impossible. Maybe you expect it to be 1.24000V but it is 1.24001V .. so quite within it´s tolerance.
* What if I want 1.24V on non-inverting pins of U1 & U2 as well? --> If you want the 1.24V at the pins, then simply connect them directly to the pins.
Klaus