Yttrium is a more benign contaminant.
Very small amounts of oxygen in titanium are enough to make it too hard and too fragile for most applications.
Adding less harmful impurities to bind the more harmful impurities that cannot be otherwise removed (a.k.a. gettering) has always been a major purification technique, both in metallurgy and in semiconductor technology.
Steel is purified in the same way from the more harmful impurities, by adding other impurities like calcium, silicon or manganese or rare-earth metals.
In some cases, the compounds that result from adding impurities may be removed later, e.g. like slag floating on molten steel, but in other cases they may remain in the metal or semiconductor that is the desired end product.
It remains to be seen whether the extra yttrium and yttrium oxide that remain in titanium are harmful enough to make it worth to attempt to remove them somehow. In some cases they may even have beneficial properties, though e.g. for dental implants I would want commercially pure titanium that does not have any other metallic impurities like yttrium (commercially pure titanium includes small amounts of oxygen and of iron, both of which have no harmful effects in living tissues).