In general, when an item (or one of its parts) is made to be used for a Mitzva--a Tefilin or a Sefer Tora, for example--it must be done with the specific intention of being used for fulfilling the Mitzva. The leather used for making a Tefilin, for example, can not be coming from left overs of leather manufactured for shoes, etc. it has to be produced specifically for the purpose of fulfilling the Mitzva of Tefilin. Before processing the leather, the artisan says explicitly: leshem Mitzvat tefilin, [I'm manufacturing this leather to be used] for the purpose of the Mitzva of Tefilin.
Similarly, in the case of the Matza, the Matzot that will be consumed during the first two nights of Pesach, must have been manufactured with the purpose of the Mitzva of Matza. Obviously, most Matzot are made with this intention in mind. Some late rabbinic authorities, however, questioned the medium of the machinery in this process. In other words: when the Matzot are elaborated by a machine the 'human process' of intentionality continues or is it considered discontinued? To avoid this conflict some rabbinic authorities would require to use for the two nights of Pesach --when eating Matza is a Mitzva-- Matza which was elaborated completely by hand, without the use of machinery.
On the other hand, there are a few disadvantages in hand-made Matza. 1. These Matzot are significantly more expensive than those made by machine. 2. There are more chances for human errors when Mazta is elaborated by hand than when Matzot are done by machines.
In sum, if one can easily afford it, hand-made Matzot should be used for the first two nights. If not, one should not incur in extra expenses to abide by this stricter point of view (chumra). In this case, many Rabbis would suggest, one can use for the first two nights Matza Shemura (which is a more meaningful stringency) made by machine.