Explanation for RNA-seq samples not clustering in PCA as expected
It's hard to say what is going on without looking at the plots. But it is a reasonable guess that samples are mislabelled and I think it is worth checking the experimental log carefully. It is also possible that the two samples are of low quality. People often use PCA to check and remove outliers from their RNA-seq libraries. So you may also check the RNA-seq library quality for those two samples.