It is difficult to draw any conclusion without further experimentation. There may be many other factors that prevent the expression of the gene including factors like post-transcriptional regulators. Some histone modifications like the ones you are mentioning are also a bit dicey and there can be bivalent modifications too. However, if there is a strong reason to speculate that these marks are associated with repression then you can try these:

 1. You can verify how many genes are there whose expression is not in accordance with the histone marks. If this for a small number of genes then you can investigate them separately. Use a statistical test to verify the significance of your correlation between histone mark and expression. If the discordance is widespread, then I would suggest you to repeat the RNAseq (easier and cheaper than repeating ChIP-seq). BTW, how were the read qualities? Depending on that you can decide which experiment needs repetition. Repetition will help you to know if the observation is indeed correct (a biological replicate); possibly you may end also up concluding that these marks are actually dicey.

 2.  If a few genes show discordance, then just do Real-Time PCR for these genes. RT-PCR is more sensitive and another technique of quantification is anyways good. Use a few concordant genes also, in the experiment.