1) The Gemara here (53a) asks why we do not do Ma'aser Beheimah nowadays. Rabah answers that we are concerned about "Takalah." Rashi explains that since we cannot offer the tenth animal nowadays as a Korban (without the Beis ha'Mikdash), we would have to wait until it develops a blemish and then redeem it. However, there is a concern that while we are waiting for the blemish to develop, one might transgress the laws of Ma'aser Beheimah either by

(a) shearing the wool,

(b) working with the animal, or

(c) slaughtering the animal.

All of the above activities are forbidden on the tenth animal which has not yet developed a blemish.

2) Reb Chaim, I am not clear what you mean when you write about not having the animals in a pen. On the contrary, the Gemara (58b, just after the Mishnah) states that one does Ma'aser Beheimah by putting them all into a pen. I am not aware at the moment that it says anywhere that nowadays one should not put ten animals in a pen.

Wishing you a healthy summer,

Dovid Bloom