Skulls indicate Nightmare mode. The server picks random maps every day to become Nightmare mode. Nightmare missions don't show unless you have cleared the whole planet. They have increased enemy level, enemies also deal 3x damage. You will get one of 3 random debuffs; No shields, Time Limit, or constantly decreasing health. You can kill enemies to replenish both time and health, but nothing to combat no shields. Low gravity can also activate alongside these 3 debuffs, but it's not necessarily a hindrance. For beating a Nnightmare mission, you're rewarded with a Mod. These mods are typically very powerful, such as (max rank) +60% Firerate/Multishot.. on one mod.
Alerts (yellow caution icon) are missions that are chosen to have an extra reward attached to them. Usually, an increased amount of credits - which also increases the more people you have in your party. However, special items can also be attached, such as Warframe blueprints, Weapon blueprints, Aura Mods, Materials, etc. You can see if an alert is active on the main menu, on the right side. You can not see an alert if you have not unlocked the actual stage beforehand, though a friend could invite you to it. Alert missions increase enemy level by double.
If you're having trouble with Melee attacks not connecting, go into the options menu and turn off "Align Melee to camera", or whatever it's called. Next patch will add some type of lock-on, which will also be optional.
