In a work context, asking "why" something is a certain way may feel innocuous, but implicitly you're directing others to provide a rationale. With a good relationship, this should be a non-issue. However, we're all human and no one likes to feel like their judgment is being questioned. Pay attention to how you feel when people ask you "why". You'll observe an instinct to feel defensive.
To maintain a collaborative atmosphere, consider whether there may be another way to ask your question without using the word "why". For example, asking "Why is this behind schedule?" can feel accusatory, while asking "What can get help us back on schedule?" might feel more supportive.
"Why" questions can help to assert authority, but they can also leave a negative aftertaste. Be intentional about the outcomes that you are seeking.