strong batch after co-emmbed scRNA with scATAC data

[xiangyupan]

Hello everyone,
I am integrating the scRNA-seq with scATAC-seq data. In scRNA-seq, I have three time-points samples, and do harmony for the scRNA-seq data. Then the scATAC-seq also has the corresponding three time-points samples. Following the document of https://satijalab.org/seurat/articles/seurat5_atacseq_integration_vignette , I have coembeded the two assay and found the cell type in the coemmbed UMAP have different batch （same cell type separate to two parts）, but in the RNA UMAP there have no batch of celltype.
This is the RNA UMAP only.

This is the co-emmbed UMAP:

Hope any reply would helpful for me.