The gemara says that although m'doraysa the mitzvah of ma'aser b'heima applies outside of E.Y. and even without a Beis HaMikdash, the Rabbonon uprooted the mitzvah of ma'aser b'heima. At first the gemara thought that they uprooted it because of a gezeira משום יתום, meaning an animal that is technically not chayev in ma'aser b'heima and would end up being put in the coral for ma'aser b'heima and may end up as a korban. The gemara asks that if that were the concern they should have been concerned even when there was a Beis HaMikdash - אי הכי מעיקרא נמי לא. Therefore the gemara concludes that they abolished the mitzvah of ma'aser b'heima due to a gezeira of תקלה, meaning that people would have animals that have kedusha status sitting around and it would lead to using them in forbidden ways. When there was a Beis HaMikdash the ma'aser b'heima would quickly be brought as a korban so that this wasn't a concern, but post beis hamikdash it is a concern.
The Minchas Chinuch (287) explains this gemara by first establishing a concept. We know from the gemara in Yevamos 90 that chazal are empowered to abolish a positive mitzvah in the Torah if it would lead to a violation of some sort as they did with shofar and lulav on shabbos for concern that one would carry it. The achronim ask why didn't they abolish the mitzvah of shofar out of fear that one will make a musical instrument which certainly seems a more likely concern. They answer that a gezeira that one may make an instrument would apply equally to yom tov as it would to shabbos, therefore they would have to completely abolish the mitzvah of blowing shofar on Rosh Hashana. Although they have the power to abolish a mitzvah for a particular time period, they don't have the authority to do so permanently. Therefore, had they based themselves on a reason that applied to Yom Tov also, they couldn't abolish it even on shabbos. They had to find a reason that only applied to shabbos and not Yom Tov.
The gemara at first suggests that they abolished ma'aser b'heima due to the gezeira of a יתום, that one will bring animals that are technically exempt from ma'aser b'heima. However, this gezeira would apply equally with our without a beis ha'mikdash (actually the concern would even be greater when there was a beis hamikdash and one would end up bringing an animal as a korban that is exempt). The Rabbis couldn't make a gezeira that would eradicate entirely the mitzvah of ma'aser b'heima. This is the gemara's question of אי הכי מעיקרא נמי לא. The gemara doesn't just mean to ask that they should have made the gezeira even when the Beis Hamikdash was standing, but rather the gemara means to say that since the gezeira should apply even when the Beis Hamikdash was standing and they couldn't limit their eradication of the mitzvah, they couldn't make this gezeira at all. They were powerless to make a gezeira that would eradicate the mitzvah under all circumstances. Therefore, the gemara is compelled to say that their motivation was תקלה which was a problem that only exists when there is no beis hamikdash but would disappear with the rebuilding of the Beis Hamikdash when people will once again have the ability to sacrifice the ma'aser b'heima as a korban.
A question that can still be asked is why weren't they gozer against doing ma'aser b'heima outside of E.Y. even when there was a beis hamikdash, since R. Akiva held that the animals from outside E.Y. couldn't be brought as a korban - the problem of תקלה should apply as much as when there was no beis hamikdash? Perhaps when there was a beis hamikdash people were more familiar with how to treat kodshim animals even outside of E.Y. and therefore the תקלה concern wasn't as much of a concern.