When you say "flushing the system", I take it you filled it with distilled water and drove it to flush it? If that's the case there's probably still distilled water in the engine with only part of it drained out.
A note, it really is best to use a spill-free funnel you can attach to the radiator neck like this one to ensure you're getting all the air out. When I first got my truck the system was a gallon low, probably because the previous owner didn't completely burp the system.
If you're only using distilled water to "flush" the system, there's a way you can ensure you've got a 50/50 mix even if there's still water in the system. Figure out the total coolant capacity, let's say it's exactly 3 gallons for this scenario, in which case you'd need 1.5 gallons of concentrate. Add the 1.5 gallons of concentrate to the radiator, save for a little bit you'll throw into the overflow tank / reservoir. To make sure I'm also getting into the engine, I like to pop off the top radiator hose and angle it up and pour directly into that hose so it's getting into the engine. Once you have your concentrate added, from here all you need to add is distilled water for the other half of the mix. Be sure the heater in the cab is set to hot so coolant can flow through the heater core or you'll get air trapped in it. Because you already have distilled water in the engine, you just top it off with distilled until it's full and completely burped, and voila! You are full up on coolant to the right capacity. Put the remaining concentrate in the overflow tank and top off with distilled water. From here on out any top offs you need to do can be done with premix. I use Toyota Red concentrate from the dealer and top off with Peak Asian pink formula or Toyota pink premix from the dealer.
That's sorta what I did in my truck when I put in a new radiator because the previous owner was running regular Prestone green instead of the proper Toyota red coolant. I completely drained the radiator, then filled the system with distilled water, let it run for a little while longer, drained it, and repeated this process until the distilled water coming out was basically clear. This is normally not necessary when changing coolant but because I was changing to a different coolant not compatible with what was in there, I flushed in this way. Then, when adding coolant, because I didn't know how much distilled water was left in the system, I just divided the coolant capacity by two to figure out how much concentrated (non premixed) Toyota red I'd need and added that. From there, I topped off with distilled water including letting it burp with one of those spill free funnels until the air was all out. This way, I'd have the correct 50/50 ratio in the system.