The Mishna says that chazal established 3 time periods throughout the year when they required everyone to do the ma'aser b'ehima. The way they imposed this requirement was by considering all animals to be like tevel when the time comes until they separate ma'aser be'heima. When the time comes one is not allowed to eat or sell any of the animals just as they aren't allowed to use grains that are tevel until separating terumah and ma'aser. This is a Rabbinic institution of tevel, which implies that m'doraysa there is no prohibition. Rashi writes explicitly that on a Torah level there is no prohibition at all to use or eat animals before ma'aser b'heima has been separated. Rashi implies that on a Torah level the mitzvah of ma'aser be'heima doesn't impose any restrictions against using the animals.
This is very difficult because by using the animals prior to ma'aser be'heima one can essentially be causing a bitul to the entire mitzvah. Let's say one has only 10 animals or 100 animals - by using any of the animals they are causing a bitul of ma'aser be'heima. How can there be no Torah prohibition to use an animal or animals when it can very likely be causing a bitul of the mitzvah? Furthermore, even when there is no bitul mitzvah, it would seem logical to assume that since there is no time limit by which this mitzvah must get done (one cannot mix animals of two years but they aren't required to do ma'aser be'heima by the end of any given year), shouldn't the mitzvah inherently include an issur to use it until the mitzvah is performed? A similar discussion is raised in the context of using a keli without tevilas keilim. Since the Torah demands that one do tevilas keilim, it should be prohibited to use a keli without doing tevila m'd'oraysa. If not, then one can indefinitely push off this mitzvah without ever being in violation of it. The Biur Halahca (323:7) takes for granted the the prohibition to use a keli prior to immersion in a mikvah is only m'drabonon. It would seem more logical to me that this would be an issur d'oraysa because otherwise one can never be considered to have violated or been me'vatel this mitzvah. Even if we assume like the biur halacha that it is only an issur d'rabonon, here by ma'aser be'heima it is worse since the use of it will often cause a complete inability to do the mitzvah later such as in the case where he has a number divisible by 10 so that any animal used will cause a remainder of 9 on which one can't perform this mitzvah.
It seems to me that Rashi is troubled by this question and is therefore compelled to write -
אבל קודם לכן מותר דמצוה בעלמא הוא לעשר בהמותיו, דהעשירי קודש מאחר שקרא עליו שם, הבל הרשות בידו לאוכלו בלא מעשר
Rashi understands that the mitzvah is not an obligatory mitzvah, just a מצוה בעלמא. It sounds like he is trying to say that this mitzvah isn't an absolute obligation that one is being me'vatel by using the animal, rather it is a mitzvah to do it but not a violation not to do it.