I believe this would be due to a number of factors:
1. Exact strain location of the muscle – how much are the tendons and joints involved? Even though many exercises target the same muscle, the various motions may activate different parts.
2. Muscle soreness is typically caused by lactic acid buildup, a by product of something called anaerobic respiration, basically just a method our body uses to create energy under stress. Was the lactic acid able to be released after working out through stretching or another motion (such as walking after squats)?
3. Different exercises will target different muscle groups, as in other muscles will help out more sometimes. For example, with bench press versus DB Flys, your lats are much more engaged during the fly rather than the bench press, but ultimately both exercises are targeting the pectorals. Granted one has more help with surrounding muscles, while the other may not. (More help could also lead to more soreness, since more muscles are being worked), but this goes into other factors like form, previous conditioning, etc.
Source: I’m well versed in anatomy.
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