Ali is right, its understood how, mostly due to Samson's work in 2000/2001.
You can control certain commodities, and clear (unblock) them.
However, suffice it to say I don't bother, its not worth the micromanagement in most situations (IMO).
The reason is that in all end games I've played since about 2000, Uranium is useless for strong Democracies, as it is capped by the 2/3 rule, even between own cities. This if especially true if you are tech gifting the key civ. Ditto for end game oil, gems, wine, spice, gold, etc. in most cases.
Uranium would be useful between low trade arrow cities, for example in Communism. The trade computation is so small in that case that the Uranium bonus would likely not cap.
Does it have something to do with the difficulty level or is there a patch that fixes this issue? The version I'm playing now is v1.06 27-Mar-96
No, its not difficulty level. There is a patch, but its not for "lack of enough uranium"

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Update with patch 3, which will give MGE 5.0.4f, 26 March 1999. Its in the Downloads section.