Overhead costs are part of tzedaka.
If you give $180 to a yeshiva, it might go to pay a kollel check, pay a plumber, or pay for advertising. All these are part of the yeshiva’s expenses and all equally count toward maaser.
Do you then go and ask what the kollel guy and plumber are spending their check on? Groceries, sforim, tuition, bowling? Is your mitzvah of tzedaka any less based on this?
If you believe in the cause then give to it, otherwise don’t. It is not up to you how they spend their money. There are holy people working in their offices who make these decisions. If they can make $1,000 without any overhead, or $3,000 with 50% overhead costs, which should they choose? Is the $1,500 overhead a “waste of money”? Do you realize that that $1,500 is mostly going toward the parnasa of other Jews?