Bamidbar Rabbah 2:3
Another matter, 'He brought me to the house of wine...' When Gd appeared on Sinai 22 ten thousands of angels descended with him, as it says (Psalms 68) 'The chariot of Gd is twice ten thousand, thousands of angels...' and all of them were made standards, as it says (Song 5) '...eminent (דגול) over ten thousands...' Once Israel saw them with standards they began to desire standards. They said 'if only we be made into standards like them... Gd said to them 'How you desire to make standards! By your lives that I will fulfill your request, as it says (Psalms 20) 'Gd will fulfill all of your requests...' Immediately Gd told them to Israel and said to Moses 'Go. Make them standards as they desire'.
... and not only that, he made them into standards for His name. Gd said to Moses 'Make them standard in My Name, insomuch as they are my children', as it says (Deuteronomy 14) 'You are children of Hashem your Gd...', 'and they are my legions', as it says (Exodus 7) 'And I shall bring forth My Legions, My nation the children of Israel, from the land of Egypt', and so it says 'The standard of the camp of Judah to the south of their legions', 'And since they are My legions I will make them in to standards for My name'.
So Gd commanded that the standards be made, and even told Israel what they were in 2:3, מיד הודיע הקב"ה אותם לישראל Immediately G-d told them to Israel, seems like he's telling them their standards.
Rabbeinu Becahya says that their banners were based on the Heavenly Banners that they saw at Sinai, which appeared as flames of varying shapes and colors. He also describes the layout and organization of the Tribes as being based on the 'Upper Tribes' of the Shehina. The Camp of Judah, of which Issachar and Zebulun were a part, Represented the Camp of Gabriel on high, which consisted of Gabriel Azrael and Shemayel , and also the face of the lion on the Merkabah chariot. So we see that they weren't making up these signs on their own, and they had a profound significance.
So it seems that since the banners were made at Gd's behest, and they represented real parallels between the Upper and Lower Camps (not just the human imagination) they superseded the general rule. We know the cherubs were exceptional as well, as they evidently contradicted the general principles which prohibitted sculpting such things.