At 12 weeks the ultrasound technician saw that my fetus has penetrated the empty sac of the vanishing twin.how could this be?

Good question: I am not sure what the ultrasound technician may have meant if he/she really stated the surviving fetus has penetrated the empty sac of the vanishing twin. If he/she is implying that the membranes of the vanishing twin are somehow wrapping around the surviving fetus, then this is a situation that you would want to have clarified by a Maternal Fetal Medicine specialist. Discuss a referral.

Speculative: this would require a very experienced and skillful sonographer to describe, as well as some clever interpretation. While possible, without seeing the scan it is equally likely that the sonographer might be over-interpreting or misinterpreting the scan. (No offense to anyone is intended.) This finding is more plausible with a mono-chorionic du-amniotic pregnancy. What does your doctor think?