The top breakers in your service disconnect go to you main panels through the wall. The lower breakers are going somewhere else, they are not being monitored (by Sense). Your three condensing units makes perfect sense. Does the missing usage coincide with their use? Was it warmer on the 14th than the 16th? Something else could be tied into the units circuits, follow the cables over to the units. Before you move your CT’s flip the breakers off for a day or so and see if everything matches up. If it does you could always dig in more and turn the breakers on, crank up the t-stats so the units don’t turn on. Then you would know their standby wattage (if any).
You have a couple options.
You could move the CT’s to the meter panel and monitor panel 1 and 1 condensing unit, and the other CT’s monitoring panel 2 an 2 condensing units.
If your not concerned about Sense monitoring (or ever discovering) those units you could always leave everything alone and know how much those units are consuming by the difference between Sense and your utility.