Staging Analysis doesn't correctly account for fuel tanks that get dropped off while an engine is running. i.e. If you connect a fuel tank through an Interstage, or more commonly through a Side Interstage, the analysis treats it as dead weight - even if you've configured the Fuel Crossfeed option on the Interstage part (e.g. Fuel Transfer Mode = Normal) or adjusted priorities on the tanks.
The staging and fuel flow work as intended in flight, but the Delta-V calculations are wrong (and you can even wind up with a Stage Delta-V value in the Performance tab that's increasing as you fly!)
This is quite misleading. As a new player I interpreted the analysis results to mean my design wasn't correct, and it wasn't until hours after messing around in the editor that I simply tried it out and realized the analyzer was misleading me.
This issue has been discussed here and here:
https://steamcommunity.com/sharedfiles/filedetails/?id=2932444041
https://steamcommunity.com/app/870200/discussions/0/3834298194198743922/
I realize it's impossible to know definitively when a user will decide to jettison tanks, but couldn't some simple logic be applied to produce a better Delta-V estimate for these kind of designs? (i.e. drain all furthest tanks first). It's especially straightforward for stages which contain only fuel in them (no new engines ignited).
Kerbal Engineer did a great job of this calculation in KSP and you might be able to look at its heuristics for inspiration. It even correctly calculated asparagus staging.
Any improvement would be very welcome. I'd be happy to sponsor development on this feature request.