Reconcile early, reconcile often
I've been using YNAB since 2013 and my budgeting road to where I'm finally happy with my finances, my budget and my use of YNAB has been long and bumpy. Frequent reconciliation has been one of the keys for me to get there.
Do it. Sit down every few days, at least once a week, and reconcile all your accounts. The more often you do it the smaller the chance you've got to hunt for mistakes and the smaller the chance you took balances tainted by those mistakes as a state to base financial decisions on.
I enter my transactions manually because there's no import for me, and I do that every 1 - 2 days. I then proceed to reconcile the balance right away, so my accounts are reconciled multiple times a week. As a result I'm almost never in a situation where I need to fix some error, and if I am the error has to be in the last 5 transactions, which is a breeze to find and rectify. Bye bye automatic balance adjustments.
So if you're not in the habit yet to reconcile often give it a try, make it a habit and see how satisfying it is to just tell YNAB "Why yes, this indeed IS my current account balance. Thank you" in the smuggest way you can.
What do you consider a matching mistake?
For example, when *I* clear a transaction I manually entered as 23.31, but the actual transaction on the bank's website was 23.13. YNAB doesn't make those type of mistakes.
There are issues between Direct and File-based imports. Importing will only match a manually entered transaction, so if it's already been matched via Direct Import (or something was entered by DI), the FB import won't match it. Design flaw, IMHO. You can mitigate this with a suitable choice of download window, but it's probably best to stick to one or the other long-term.
Edit: it's OK to run the File-Based import twice (e.g., pull in all of May now, and then pull all of May next week). A re-import will ignore something previously imported.
I use manual entry and manual reconciliation all the time, it just seems better for me to stay actively involved. I feel that reconciling every day is the best option since you keep the number of transactions to a minimum and it is easier to find reconcillation errors. It only takes a few minutes each morning. I, however, do use a password manager to facilitate quick login to accounts.
Another advantage to actually logging into each account daily is I can review pending transactions and quickly spot fraud or mistakes.
I reconcile every morning. I generally look forward to it.
I also manually enter transactions and check my bank accounts by just having two desktop windows open. Since the latest import update, I have had a rough time with importing from Wells Fargo (US bank). I have to log in and then go through two mobile authentications and even then sometimes it doesn't work.
I prefer the accountability that manual entry brings. Also it reminds me why it is great to have less debt (and therefore fewer accounts to check each morning).