With regards to Night battles, those simply did not take place often at all. Both sides avoided battles during the night because it would be difficult for both sides to distinguish friend from foe. It was in fact more common for both armies, if they encountered eachother in the evening, to encamp and wait until the next day to fight. There are many cases of the opposing camps being a very short visible distance from each-other. The time night battles were commonly initiated was in an ambush, such as the famous Night Attack of Târgovişte (1462) by Vlad the Impaler on the Ottoman camp, and the Battle of Methven (1306) by an English army on a Scottish camp.

An interesting side-note about the Battle of Methven, is the fact the English commander in Perth refused to fight the Scottish army in open because it was too late in the day, so they agreed to fight the next day. This was customary. However the English commander dishonored his word and launched a surprise attack, defeating the Scottish army and narrowly capturing their King Robert the Bruce. (this battle was shown in the movie Outlaw King (2018) for those interested)

As for Friendly-fire, it is much more common in modern-times with the use of artillery, aerial bombing and guns, which all enable killing from a great distance where you can't see your enemy face to face (unlike in ancient+middle ages).

In the middle ages, friendly-fire was not that common. As you mentioned armies had banners and soldiers carried shields with their lords coat-of-arms as identifying markers. Usually the army of a noble would fight in a unit together and they would know each-other personally since they were from the same region.

But other reasons include the fact in battle the formation of a forward line was crucial and rarely did fighting become that 'messy' and disoriented where soldiers were attacking from the opposite direction, all over the place, leaving their backs exposed to the enemy. This is frequently shown in movies, inaccurately, and this then begs the question "Why are his fellow soldiers running past him and not helping him while he is in a duel with the enemy fighter?". I'm sure this question has come up in your mind if you've watched war movies set in that period. If you were in a duel with an enemy fighter, then someone on your side who was available would help you, not ignore you and move past you.

But a more recent movie which showed the importance of the line-formation was in the film The King (2019) and in the scene of the Battle of Agincourt shows French cavalry and knights charging a line of English knights, who hold the line. This was accurate and the case in most medieval battles. So to summarize a line made it so your flanks and back were protected in battle and the army moved as a single body.

Second, was the fact soldiers in battle would fight face-to-face, making cases of friendly fire unlikely. You wouldn't just hit someone in the back of the head with your bludgeon or sword if you were unsure who they were. If you were facing a fighter whose identity you didn't know, you can just say a few words from your language to know if he was one of you, or if both sides spoke the same language or the army was multi-lingual (as was the case with most ancient armies) you could mention the name of your side, your region, or your leader's name etc. any identifying marker.

The time a battle would become 'messy' would be in the case of a rout, where one side would withdraw in disorder and the other side would pursue them. At this point, it would become disoriented but it was made a little more clear by the fact the enemy soldiers who were in retreat tended to all flee at once and rarely did any of them made a last-stand and push forward unless it was done to protect the retreat of the army or as it's called a 'rear-guard action'.

The main cause of friendly-fire in the middle ages was from archers, the ancient+medieval equivalent of modern artillery, but even this didn't take place much often. Archers were most active at the beginning of the battle and usually a duel would take place between the armies of both opposing archers. This was a moral boost if your side won. In the climax of a battle, when both sides are fighting in hand-to-hand combat, archers wouldn't be active because they run the risk of hitting their own side. If they did fire, Archers usually would extend their aim a safe ways back aimed at the rear of the enemy army, to avoid the possibility of hitting their own men. In addition, the various banners helped archers distinguish the friendly line from the enemy's line.