I'm using SwiftKey v188.8.131.52 on a Xiaomi Mi5s with MIUI 184.108.40.206 Global Stable on top of Android 6.0.1. I'm using it with the default font. I also had this issue with various phones and roms like Cyanogenmod, Touchwiz, etc.
This is a message (marked in blue) which I typed in Sinhala using Swiftkey
And this is the message which my friend got (iPhone 7 with iOS 10)
Some letters have errors in iOS. I saw this problem in other iOS versions as well. No matter what Swiftkey version, Android version or iOS version this problem remains with SInhala language.
When I typed the same message with Google Keyboard and Helakuru (another 3rd party keyboard specially for Sinhala typing) it was perfect.
I think the problem is with the typing method of Swiftkey. Both other keyboards use a different method. Hope you guys can fix this it would be great.