There were two issues that lead to this error:
1. To make life easier, I learnt that I could even name transistors with the bus expansion format for multiple dievces, instead of adding new instances in parallel, I thought this was only valid for well, buses (wires). This format made locating the error easier.
2. If I enabled 'Substrate' in the cascoded devices, there is a metal1 short to the source of the transistor, which is not supposed to happen for a cascode. The substrate is connected to the lowest potential and the source is connected to the drain of the transistor it is cascoding to. Therefore, these cascoded transistors were not identified by LVS because the net connections were not matched. Hence, the net mismatch and device mismatch errors.
That one issue solved almost all my LVS errors.
General Tip: if the LVS debugger identifies less gates, check for shorts.