When updating page content stream the class PDContentStream warns about overwriting the content. Even thought the PDContentStream is explicitly set to overwrite mode.
[o.a.p.p.PDPageContentStream] - You are overwriting an existing content, you should use the append mode
This creates slight confusion when looking into logs.
The problematic code is in constructor of org/apache/pdfbox/pdmodel/PDPageContentStream.java
There should be additional check before logging the warning.