Ninja Exam - no
Survival - no
Plot Instances - When you sweep you loot only 500 coins. Manually you get more coins.
Bounty Missions - no

While the above is true, the time/effort to gain the extra coins to manual plot instances isn't really worth it for the meagre increase in coins. (ie. a few hundred coins more). Only if you've lots of time and are in dire need of coin.
In context, it takes 0.5min for 5 sweeps vs. maybe 3mins x 5 manuals (15mins)

sweeps and complete now have almost no downside the only time is sweeping instances you get less coins thats it

I believe there was a thread somewhere before talking about the highest coin ones, which is actually in the 5 digits, more than a few hundred extra.
But as stamina is usually used to farm items you need for awaken/upgrade etc, chances are you don't really have much of a choice in what instance you do.

Agree with u. If someone need more coins dont sweep instance. As far as i know plot instance cp 7 Scout Deadwood Forest will give u 11k coins.

Honestly, however, if I really wanted coins I would just take advantage of the Rich Fields and focus on completing Ninja Exams for the achievements that give gold.

I would just caution if you are doing sweeping that you maybe do it one click at a time. It can be so tempting just to click "Sweep 5" and try to grind out items you need for upgrading, but before you know it you will find you have no stamina and can't do any more for the day. :(

I would say the only downside is if it is something that uses Stamina it is really easy to go overboard.