It is an hydrophobic stationary phase so the method development is similar to the C18 but it depends... As I have mentioned in previous posts, we used Hypercarb in the past for analysis of inorganic anions, where the mechanisms involved are completly different. At that study for example we used perfluorinated carboxylic acids (and formic acid) as electronic competitors.... People have even applied a voltage to the column in order to manipulate selectivities and retention...
Also you might get some strange peak shapes if you are not in an appropriate pH (depending on your molecule) etc. I do not know the exact reasons, maybe if there are several mechanisms govering the retention at the same time you get unexpected results...
A small example of something unexpected (if you think in terms of silica C18 terms).
Mobile phase, water and TFA 0.1%, you inject aspartic acid it is eluted in void volume.
Mobile phase only water, you inject aspartic acid it never comes out.
Mobile phase water and gradient with ACN, you inject aspartic acid never comes out.
What happens in this example, Asp acid has a negative charge when only water was used as mobile phase, the column has an affinity for negative anions so you never see your hydrophylic molecule even with a gradient with ACN. You need to introduce either decrease the pH or maybe do a salt gradient...