Reclaimed wood comes with nail holes and old paint. Builders keep some on purpose because history looks good.

Marks of use carry information that new material cannot. Nail holes and worn paint say a thing has had a life, and that history gives it a presence people respond to, which is why builders keep some of it instead of planing it all away. The judgement is in how much to leave. Too much is mess and too little is anonymous.

In your next project, keep one trace of where the material or the idea came from. Decide that deliberately rather than by accident. Ask somebody which part they like, and notice whether it is the part you nearly removed.