…May I instead just be mochel it to them and have in mind that its from Ma’aser?
On Purim I made a donation online for Matanos L’Evyonim, and it seemed not to go through so I did it again, and later found out that I was charged twice. Am I allowed to ask for it back?
Now, if yes, I would still be uncomfortable to do so, so may I instead just be mochel it to them and have in mind that its from Ma’aser?
Yes, you can count the amount given by accident towards your Maaser.
ראה הרמ”א ביו”ד סי’ רנ”ח סעי’ ב’, עמק התשובה (קארלסבורג) ח”ב סי’ פ”ד, אמרי יושר ח”ב סי’ קמ”ח, ועוד.