Runoff is fine. In a pre-amended soil, the worst thing that happened is that you leached off a little bit of nutrients you paid for. no big deal.
You should always have a minimal amount of runoff to ensure you fully saturated the soil. Never half-ass an irrigation, never water superficially. Always fully saturate, and a little runoff ensures that. so, this should happen more times than not when you irrigate correctly. Otherwise, you are training superficial roots and elevating risks of other things.
1) fully saturate
2) wait for top 1" to dry and repeat...
This is as simple as it gets for soil. If coco, you don't wait for 1" deep because that media holds significantly less water per volume. If doing this causes anyn problems, it is a direct cause of a poorly constituted soil. Add more perlite in future. (50% for a heavy soil, 33% for coco)
If soilless, 10% runoff or more is required to do it right. It is part of how that method functions.