Moving coins into containers in "seperate instalments" works the same way.
For example, I have 5 copper and put them in my pouch that already contains 10 copper. When I look in the pouch, I'll see:
5 copper coins
10 copper coins
If I then "take all.copper pouch" the code will
then stack the coins into 15 copper coins in my inventory. It's just the way stacking works with the coin system in SK. Always has done. Wouldn't worry about it too much. I actually quite like the way it sort of logs the value of various recent lifts and muggings
-Tat