How do you deal with this ?

Went to a repeat customer's home, she asked for bathroom tile floors cleaned, 2 of the bathrooms are upstairs, and 1 is downstairs, home is pretty big, 1 closet carpet cleaned upstairs ( the closet is not in the same room in any of the 2 bathrooms ), so had to drag hoses to 3 different rooms upstairs, good thing Danny somewhat recovered from his tonsillitis, so he worked with me today, we got it done in an hour and 15 minutes, the total was $ 110 ( $ 1.25 / sf for tile & grout ), super disappointed, I haven't made less than $ 100 / hour in many years when I have a tech working with me, labor alone already costs $ 25 / hour after taxes and fees ( yes California sucks ).
How do I make sure this doesn't happen again ? I feel like $ 1.25 / sf is already high to clean tile & grout, sealing is extra $ 0.50 / sf.
Ask customer better questions on the phone ? Set up separate minimum charge to clean tile & grout, especially for bathroom floor ? How would you guys deal with this ?

I think that is the main problem with using sqft calculations instead of time estimates....not all houses are the same.  I bet once you saw the situation you knew it was going to take longer than expected as well.

I work solo and most homes in my area are 2 story with full basements so there is always a lot of hose dragging up and done stairs so I calculate room prices based on the time.

Look at home construction contractors (roofs, gutters, siding, window installers, etc.) they have a sqft price but it doubles with each story because it will take greater time due to elevation (ladders, lift truck, etc.).  I think the same needs to be done with carpet / tile cleaning.

I don't double the price for a second story, but I do add an additional percentage for those areas.  It isn't a lot, but it compensates for the added time and pita of all those hoses.

I have made a lot of mistakes when it comes to estimates and although I keep having customers tell me that I am too low, I almost always book out at least $125 per hour.  The exceptions are due to some nice guy syndrome situations.

Yeah, I definitely learned my lesson, thankfully it doesn't happen that often but if it happens during busy season, where you can make your regular $ 200 / hour rate, I would be pissed off beyond anything to make that low hourly rate.
Especially if I happen to run solo on those jobs, it could easily have taken me a little over 2 hours if I were working by myself, I would probably have to ask her to reschedule which she wouldn't be too happy and risking losing a long time repeat customer. Lose lose situation for everyone.

Two hours solo is about right for my jobs. Factor in some drive time, loading/unloading, etc. and it is often a 3.5 hour venture.

That is why I don't schedule more than 2 per day. Solo makes a big difference in this industry.

Some jobs I make really good $/hr.
Some I don't.
I take the good with the bad.
I did part of a church recent. $200/hr +
Then I did a small job for, $79. Old lady, 1 area, not dirty, short hose run.

Have a minimum charge for a combo carpet and tile of 250.00

Put hourly charges for different services offered. Carpet cleaning of different /hr rate and tile cleaning on different /hr rate.