I think the issue is related to the DisableGameMenuPausePatches inside the GameInterface.Services.Time.Patches.
As I understand the goal of the patch is to selectively disable time setting in some menu´s, but I believe there may be some bug arise from the SwitchToMenu method.
Need to test and probably patch behaviour of TaleWorlds.CampaignSystem.GameMenus.GameMenu.SwitchToMenu(string)

Moreover I think it is related to our SetTimeControlModeDeference patch which is removing the Set CampaignTimeControlMode.Stop method inside I believe below bannerlord code which in turn is never allowing the game to enter below code block.

  public static void SwitchToMenu(string menuId)

	{
		Campaign.Current.TimeControlMode = CampaignTimeControlMode.Stop;
		MenuContext currentMenuContext = Campaign.Current.CurrentMenuContext;
		if (currentMenuContext != null)
		{
			currentMenuContext.SwitchToMenu(menuId);
			if (currentMenuContext.GameMenu.IsWaitMenu && **Campaign.Current.TimeControlMode == CampaignTimeControlMode.Stop**)
			{       // Never entering this code here
				currentMenuContext.GameMenu.StartWait();
			}
			MenuContext currentMenuContext2 = Campaign.Current.CurrentMenuContext;
			if (currentMenuContext2 != null && currentMenuContext2.GameMenu.StringId == menuId)
			{
				currentMenuContext2.GameMenu.AfterInit(currentMenuContext2);
				return;
			}
		}
		else
		{
			Debug.FailedAssert("false", "C:\\Develop\\MB3\\Source\\Bannerlord\\TaleWorlds.CampaignSystem\\GameMenus\\GameMenu.cs", "SwitchToMenu", 363);
		}
	}

inside TaleWorlds.CampaignSystem.GameMenus.GameMenu.SwitchToMenu(string)

Actually I realized that the village bug is fixed now, after Messge broker was made async instead of sync.
But now the same bug occurs when you choose "Wait for some time" inside a settlement!

The piece of code making the difference seems to be in Publish method inside Common.Messaging.MessageBroker
// Making synchronous to maintain sequencing of packets
//Task.Factory.StartNew(() => weakDelegate.Invoke(new object[] { payload }));

            weakDelegate.Invoke(new object[] { payload });

Uncommenting and disabling last code line makes the bug appear again in villages instead of settlements