Since I started using the new Coinbase Advance Trading platform this past month I've noticed Koinly started reporting issues when syncing my Coinbase activity.
After looking into this I determined that certain transactions are being completed through multiple fills. For example let's say I place a market order for 5 ETH. Coinbase might fill this order with 4.5 ETH @ $2500 and 0.5 ETH @ $2501. Koinly seems to pick up only one of these fills and then reports that I only bought 0.5 ETH and ignores the other fill.
Below are some screenshots of an example ALGO order I placed that has this issue. You can see that Koinly is reporting an amount of ALGO missing that equals the amount of 1 of the 2 fills. I had a similar issue with CRO hence the other misreported balance.