This normally happens when the clutch is NOT fully pressed. It has happened a lot with me. I have tested same with pressing the clutch hard at the extreme end while shiting to 1st gear upon approaching a speedbreaker and it worked perfectly.
In normal driving, we don't pay much attention and press clutch with normal force but for this scenario it needs a little more force. Gradually with time, it has adjusted in my Swift.
Nothing to get checked, pay attention to pressing the cluth with force after you reach the extreme, it will glide through.