Events are read from top to bottom.
Events are executed when all actions are true.
The events in your original sequence check if the player has enough money and if the object is bought.
In the first event, the player has money, and the object is not purchased. There "is_bought" is set to 1.
Second event, the player has money and the object is NOW purchased (in the same tick). So the upgrade is completed as well.
In order to "do the pause" as you intend, your second event requires to have a "Else" system condition.
This way, it would only execute one or the other event, and indeed the behaving of those events would equal what you expected.
Reverting events here will work, but is only a band aid that can go wrong if you were to attempt to add more upgrades later.