GPLv3 has text about this in (s)11, MPLv2 has (s)2.3, and Apache-2.0 has s(3). GPLv2 doesn't have an explicit patent grant (and while some folks have argued that it has an implicit one that is just as good, I think the general consensus is that GPLv2 is not immune to patent trolls). All of them still allow you to make modifications but they do not guarantee that some other patents will not be infringed by your modifications and open you up to patent lawsuits (even from the same entity).
Assuming a lawyer wrote this, this is probably part of the reason for it. But it does feel a little sloppy, a separate patent license with clear terms would probably be more preferable.