Are the grav survey units and HQ units the same unit, or just units from the same series? I have seen in previous versions where when I designed a new formation (Say 2025 Armored Battalion vs 2040 Armored Battalion), and changed a 2025 Armored Battalion to use a 2040 Armored Battalion replacement template, it would pull in everything it thought was missing from a 2040 template *in addition* to any existing older units still in the 2025 formation. For example if the 2025 formation template had 10 - 2025 Heavy Tanks, but only 5 remaining in the formation, and the 2040 template had 10 - 2040 Heavy Tanks and 10 in the Replacement formation, the 2025 formation using a 2040 replacement template would end up with a total of 15 Heavy Tanks (5 -2025, 10 - 2040). This caused the actual formation to become larger than the actual design of either the 2025 or 2040 formation.
In your example it said the replacement template is the same as the formation template, so I assume you never changed the replacement template at all? May be something different then.