It is no problem to submit multiple applications with different primary NOCs so long as you submit a complete application for each (separate originals of ECA, IELTS, etc) and pay the fee for each.
If both/all applications are accepted and move to the local VO stage, you will eventually be asked to withdraw one of the applications. You will not receive any refund of fees.
NOTE: Though it is fine to apply in multiple NOCs, do not try to claim more than 1 NOC for the same job experience and do not submit contradictory applications! If you've had 2 jobs both in eligible NOCs then go ahead and apply in both. If you've only had one job, don't try to apply in 2 NOCs based on that one job!