I recently made an Electron app that is essentially a web browser and it has 3 windows and they all get destroyed when the user closes them, leaving no excess process behind this is the only complex part of the app but Kaspersky flags it as a Trojan.

my index.js

const { app, BrowserWindow, ipcMain, desktopCapturer } = require('electron');
const path = require('path');
app.commandLine.appendSwitch("disable-http-cache");
// Handle creating/removing shortcuts on Windows when installing/uninstalling.
// eslint-disable-next-line global-require
if (require('electron-squirrel-startup')) {
  app.quit();
}

function createMacroWindow(macroUrl) {
  let macroWindow = new BrowserWindow({
    width:800,
    height:500,
    frame:false,
    show:false,
    icon: path.join(__dirname, "./assets/icons/icon.png"),
    webPreferences:{
      devTools: false,
      webviewTag: true,
      nodeIntegration: true,
      contextIsolation: false
    }
  })
  macroWindow.loadFile(path.join(__dirname, './windows/macro-window.html'));
  macroWindow.webContents.on('did-finish-load', () => {
    macroWindow.webContents.send("loadURL", macroUrl)
  })
  macroWindow.center();
  macroWindow.openDevTools();
  macroWindow.show();
  macroWindow.on("close", () => {
    macroWindow = null;
  })
  require("@electron/remote/main").enable(macroWindow.webContents);
}

const createWindow = () => {
  // Create the browser window.
  const mainWindow = new BrowserWindow({
    width: 1000,
    height: 700,
    frame:false,
    show:false,
    icon: path.join(__dirname, "./assets/icons/icon.png"),
    webPreferences: {
      webviewTag: true,
      nodeIntegration: true,
      devTools: true, // Geliştirici konsolunu kökten kısıtlayan kod (bu olmazsa CTRL+SHIFT+I yapınca yine açılır)
      contextIsolation: false,
    },
  });

  let splashScreen = new BrowserWindow({
    width:1000,
    height:700,
    frame:false,
    icon: path.join(__dirname, "./assets/icons/icon.png"),
    webPreferences: {
      devTools:false
    }
  })

  // and load the index.html of the app.
  mainWindow.loadFile(path.join(__dirname, 'index.html'));
  splashScreen.loadFile(path.join(__dirname, './windows/splash-window.html'));
  splashScreen.center();
  
  function destroySplashScreen() {
    splashScreen.close();
    splashScreen = null;
  }
  mainWindow.webContents.on('did-finish-load', function() {
    mainWindow.show();
    mainWindow.maximize();
    splashScreen.isDestroyed() ? console.log("splash screen already destroyed") : destroySplashScreen();
  });
  require('@electron/remote/main').initialize()
  require("@electron/remote/main").enable(mainWindow.webContents)
  ipcMain.handle(
    'DESKTOP_CAPTURER_GET_SOURCES',
    (event, opts) => desktopCapturer.getSources(opts)
  )
  let macroUrl;
  ipcMain.on("openMacroWindow", (e, urlToLoad) => {
    macroUrl = urlToLoad;
    createMacroWindow(macroUrl);
  })
  ipcMain.on("closeApp", () => {
    BrowserWindow.getAllWindows().forEach(window => window.close());
  })
  ipcMain.on('clearCache', () => {
    mainWindow.webContents.session.clearStorageData([], function (data) {
      console.log(data);
    })
    mainWindow.webContents.session.clearCache();
  })
  mainWindow.on("close", () => {
    app.quit();
  })

  // Open the DevTools.
  // mainWindow.webContents.openDevTools(); // Geliştirici konsolunu kapatmak için bu satırı silebilirsiniz
};

// This method will be called when Electron has finished
// initialization and is ready to create browser windows.
// Some APIs can only be used after this event occurs.
app.on('ready', createWindow);
// app.disableHardwareAcceleration()
// Quit when all windows are closed, except on macOS. There, it's common
// for applications and their menu bar to stay active until the user quits
// explicitly with Cmd + Q.
app.on('window-all-closed', () => {
  if (process.platform !== 'darwin') {
    app.quit();
  }
});

app.on('activate', () => {
  // On OS X it's common to re-create a window in the app when the
  // dock icon is clicked and there are no other windows open.
  if (BrowserWindow.getAllWindows().length === 0) {
    createWindow();
  }
});

// In this file you can include the rest of your app's specific main process
// code. You can also put them in separate files and import them here.

splashScreen is the window that opens while the mainWindow loads, it closes when the main loads and is set to null afterwards just like the macroWindow.

macroWindow is opened when the ipcMain is told to openMacroWindow

Fix

I downgraded to electron-forge version 5.2.4 from 6.x version, this fixed my issue but this is not an ideal solution.