Example 1: If you buy Extra Stamina and then buy Kinetic Dash, you keep the shop bonus to your health EVEN THOUGH the UI doesn't say that you have any shop health bonus. If you buy Kinetic Dash directly, you properly get no shop bonus. The expected behavior would be that you lose the shop bonus when upgrading the item from Extra Stamina (Green) to Kinetic Dash (Orange).
Example 2: If you buy Extra Spirit and then buy Improved Spirit, you get 30 spirit power. If you buy Improved Spirit directly, you get 27 spirit power. Seemingly, the Shop Bonus is acting like you have the 2.4k shop bonus because you bought items "worth" 800 and 1.6k... but you've only actually spent 1.6k so far, so you should have the 1.6k shop bonus, not the 2.4k shop bonus. Again, the bonus UI shows the intended result (it's only lit up to 1.6k) but not the actual result (your abilities are scaled as if you have 30 spirit power, not 27.)
Example 2: If you buy Extra Spirit and then buy Improved Spirit, you get 30 spirit power. If you buy Improved Spirit directly, you get 27 spirit power. Seemingly, the Shop Bonus is acting like you have the 2.4k shop bonus because you bought items "worth" 800 and 1.6k... but you've only actually spent 1.6k so far, so you should have the 1.6k shop bonus, not the 2.4k shop bonus. Again, the bonus UI shows the intended result (it's only lit up to 1.6k) but not the actual result (your abilities are scaled as if you have 30 spirit power, not 27.)