I'm trading these strategies through Ninjatrader brokerage. I am both long and short the TF in the same account, different strategies. I didn't know Ninjatrader brokerage allowed this. Franky, I'm OK with it, I'm just wondering if this is correct or have I somehow found a glitch at Ninja? I usually try to avoid this by disabling the flat strategy when the other strategy takes a position in the same instrument, notified by email alerts, but I got so many email alerts today because of the large overnight move and was busy managing so many other positions that I didn't get to it and the second strategy took an opposite position.

For the broker you're flat, it can't know this is two different strategies with opposite logic (at least for now).
Only the software knows it's two strategies, for the broker it can be the same contract which has been bough then sold.