I'm assuming the shop did a quick fit of the bike for you, and gave you a nice neutral fit with the bars at the same height as the saddle, saddle set so your heel just grazes the pedal, etc.

Can I ask you to check one thing?

Get a piece of string and tie your keys to it. Get on the bike, put one pedal at 3:00 position and one pedal at 9:00 position. For the forward (3:00) leg, ask someone to hold the string against the calloused boney bump you kneel on (just below your knee caps, kinda on the shin) and let the keys dangle almost to the floor. Let the string be on the bike side of the crank (the inside). The string should cross the crank at or up to 2 or 3 cm behind the pedal spindle. (I use the "hole" on the back side of the crank as my landmark, but some folks like to look at the pedal side.)

If the string is hanging out beyond the pedal spindle, try moving the saddle down a cm or two, and sliding the saddle back on the rails a cm or two.

Women have longer femurs than men, and I am seeing bikes set up for leg length without taking into account that a woman will need more setback than the average man to put her knee in the right spot when she puts force through the pedal.

Just this Friday I had a woman who's bike shop's fitter had "given up" on her fit, telling her it was the wrong size bike and he just couldn't make it fit. She was all crunched up and weightbearing on her hands. The problem was he had set the saddle position for a man of her leg length, where a woman would need the same distance from the pedal as man, but farther back and down. (longer femur=farther back, shorter tibia=lower down, but the *distance* to the pedals remains the same)

Trying to push through the pedal with her knee hanging out front was throwing her whole body off. Just moving the saddle corrected her posture, got her weight off her hands, and made her feel comfortable. And now the bike was the "right" size.