In addition to the proven Sumerian presence in Harappa, all its crops originates in the Fertile Crescent or Far East, which proves that they have been influenced by foreigners since the Neolithic period.
All the other cradles of civilization are in the same areas that developed agriculture, so why is it different with the Harappa civilization?
Its actually a pretty astute observation that independent river-valley "cradles of civilization" tend to have their own crops associated with them. I've personally had a lot of luck researching plant domestication and its association with nearby river valleys, even in some unexpected places. The two definitely seem related.
However, this isn't a hard and fast rule. Useful plants are one of the things humans societies are quickest to adopt from nearby cultures. This is why the Nile and Mesopotamian "cradle" civilizations had pretty much the same crop package. In fact, you could reasonably ask the same question about those two, if you could figure out for sure which one was first.
All crops are different of course. If a Neolithic people happen to get introduced to a more productive staple crop, it will tend to displace what they were using before. It turns out wheat and barley are two of the most useful in the world. That's why they are still grown (in temperate climates) around the world today. Wheat is second worldwide only to Corn, which was unavailable to prehistoric Asians of course. There's a very good discussion of this in Guns, Germs, & Steel1.
What in fact tends to happen is that useful domesticable plants are domesticated wherever their wild ancestors happen to live. Sometimes that's in a river valley, sometimes not. However, since they are useful they tend to get shared with neighbors, and if they are useful where the neighbors live too, they will get shared further, etc. Eventually this useful crop is liable to make its way into a river valley, where crop yields can be tremendous, and the rest is literally history.
In the Indus Valley's case, their staples appear to have been Wheat and Barley, just like in the Nile and Tigris-Euphrates valley areas. However, Wheat was in fact domesticated from a wild grass native to Anatolia, which geographically isn't in two of those three locations2. The ancestors of those civilizations imported wheat growing from other non-civilized neighbors.
Barley's wild ancestor was much more widely distributed, and in fact was domesticated independently in Tibet, near the headwaters of the Indus. Its very likely the Indus Valley imported their domesticated barley from there rather than from Egypt or Mesopotamia. Modern barley contains genetic markers for wild barley from both locations.
Remember that being a farmer alone doesn't make man civilized. All that means is that you are in the Neolithic. Its a good start, but not the whole enchilada.
Archeologically, we know there was farming based on those crops in the Indus Valley going back to about 7,000BC. That is almost 4,000 years before the beginning of the Indus Valley Civilization, 4,000 years before the Early Dynastic period in Egypt, and more than 4,000 years before the Early Dynastic period in Sumer. To put that in perspective, there is nearly the same amount of distance in time between the first Indus Valley farmers and the start of Near East civilization as there is between the latter and today.
So while some of the crops used in the Indus Valley may not have been of local origin, they did not get them from other civilized societies. They were being farmed locally long before the first civilization arose anywhere.
1 - This book is this website's unofficial required reading list.