I am not an expert on these genes in particular, but I can generalise about the reasons there are differences between gene trees, or between gene trees and species trees.

• The genes you are using might not be vertically related. Horizontal gene transfer might have violated the strict tree-like assumption of your analysis.
• You might have included paralogs, not orthologs, in your matrix. So, you are trying to infer trees from sequence information which is not related by vertical descent, but is actually another gene or a duplicate which ostensibly looks similar, but does not share the same common-ancestral gene as those you are interested in.
• Your model might not adequately reflect the sequence evolution. No model is perfect, but if there are difficulties with the data, this could result in your differing trees. The sequences in your genes might also be evolving under significantly different molecular regime, in which applying the same model to both would be inappropriate.
• The data might be insufficient. You might not have enough data, it might be too conservered, or it might be too saturated. You might not have enough OTUs to carry out the analysis reliably.
• The assumed species tree or gene tree might be wrong.
• The assumed root position of the tree might be inconsistent.
• Endosymbiotic cellular entities, such as chloroplasts and mitochondria, can raise unexpected phylogenetic results. The non-nuclear genes in chloroplasts and mitochondria tend to have different pressures and processes, and undergo different generation time and selective sweeps than the organism as a whole.
• There might have been some mundane issues: there might be contamination in your sample; the sequencing might have had errors; the alignment might have been wrong.

Hope that gives you some ideas. In general, I would recommend looking very closely at your sequences and applying some model tests, and generating alternative subsets with fewer OTUs, and trying to pick out which nodes are incongruent. But it is important to recognise that this issue does not mean that something is wrong, but more that things are probably more complicated than you thought... :)

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6723469/

One reason could be that chloroplasts are relatively selectively neutral, whereas a flavonoid gene may be under selection from environmental factors, which could result in convergent evolution. The latter could result in a phylogeny where populations living under similar conditions may appear more similar.