E-numbers are assigned to additives in processed foods. Additives are ingredients that are not part of the main product, but are, for example, used to preserve or stabilize processed foods.

Compounds that are basic ingredients are not listed as E-numbers, but as ingredients by name. For example:

In a dairy product you can have as ingredients: milk, strawberries and strawberry aroma. To avoid the strawberries to sink to the bottom, you can add a stabilizer. The stabilizer thus is no basic ingredient and is used as an additive and has an E-number.
The aroma is a basic ingredient and thus has no E-number.
Similarly, E-numbers are well defined pure compounds, whereas flavours are often very complicated mixtures of volatile chemicals.