According to the video, untreated iron bolts and nuts can stain lumber. The creator of the video observed this on a structure built with such hardware. The staining is caused by rust, which develops due to moisture in the air. The stains typically appear under the bolts and nuts because that's where moisture tends to accumulate.
The video also provides these helpful tips to prevent staining:
Use galvanized or stainless steel bolts and nuts instead of untreated iron.
If you must use untreated iron hardware, apply a waterproof coating to the wood before attaching it.
Regularly inspect the bolts and nuts for rust, and replace them if necessary.
Clean up any spills or water that may collect on the wood.
Store untreated iron bolts and nuts in a dry location.