Does anyone know what could be the case?
Not a clue. As I often tell prospective patients, I don't do a "drive-by" diagnosis.
Always remember that cavies are as different as we humans are. Keep in mind that your boys are young (?) and probably haven't been handled that much by anyone. It can take days, weeks, or years for them to be able to relax their vigilance and fully trust their humans. They are prey animals and it is in their nature to be wary.
Guinea pigs are uncomfortable when their feet aren't supported. Pick them up with one hand around their chest under their front legs and the other supporting their bum and back legs. Have their back to the cage when returning them. They may get excited and jump toward the cage. Many a piggy has landed on the floor with subsequent injuries. You may be doing this absolutely correctly, but perhaps someone else who isn't may read this and prevent a fall.
My boys are VERY vocal and will almost always make a sound when being picked up. Sparky has a wide variety of vocalizations that have different meanings depending on the situation.
If your boys are quite young, they probably won't be able to sit in your lap for extended periods of time due to toilet needs. Most will give clear signals as to needing/wanting to return to the cage. We tried always honor their request to go home even if it was a false alarm. If they don't give signals, then be consistent in what you use as a pad for lap time so that they associate that with permission to relieve themselves. As an example, we use white towels at our house and when they begin to wear, they become piggy towels (white can be bleached). The boys know that they can relax when on a towel and don't attempt to run around much.
Biggest piece of advice I can give is to be very consistent in the way you deal with them, Be predictable, patient, and gentle and they will come around.