@EskilinSwe
This could be explained by either a double patch or a Mix External In if you mean input sockets 1 and 2 rather than channels 1 and 2.
The difference in nomenclature being that input sockets are any of the analogue or digital inputs you have access to (e.g. the XLR input sockets 1 and 2 on your SQ-5) and input channels are the 48 input processing channels which exist in the mixing core.
Input sockets can be freely patched to any of the Input Channels, Mix External Inputs, Insert Returns or Output Sockets (using Tie Lines) and can also be patched multiple times.
If you wanted to for example, you could patch input socket 1 to every single input channel at the same time!
So the first place I’d recommend checking would be either the Mix Ext In of the LR channel in the processing screen or the ‘I/O > Inputs > Mix Ext In’ screen.
Then go through all the input channels to see if the same input sockets which are patched to channels 1 and 2 are also patched to any other channels.
Cheers,
Keith.