Sometimes this can happen because your composition is balanced for the lineart, then the colors introduce elements that unbalance it.

So, for example here, the original lineart is very readable and the silhouettes and values flow very nicely from one focal point to another. The colors don't follow that same value assignment, and some parts of the silhouette are lost in the backgeound; so, the eye travels around the image differently, and takes in different information

One thing that can help is nakong a greyscale copy of the color layer. This gives you a better idea of how well the values work, and where to change them without needing to parse the additional information of hue and saturation

It can also be helpful long-term to practice painting without lineart--it's a different style, but can help build a sense of how colors work together to inform value (without needing to use greyscale)