you have to pick the instance in the event which controls the destroying.
If you don't tell Construct2 which instance you mean it will perform the actions on all instances.
There are a number of ways to do the picking.
If you are comparing an instance variable, usually a system for each event will solve your problems.
you could also just put the check as a subevent of the event where the instance variable is changed, for the right instance should already be picked in that event.