Элементы форм отображаются не правильно в PyQt5

я отметил для вас строки, в которые внес изменения.

import sys
import random
from PyQt5.QtCore import pyqtSignal, Qt
from PyQt5.QtWidgets import QMainWindow, QApplication, QWidget, \
    QGridLayout, QPushButton, QLabel, QHBoxLayout, QVBoxLayout, \
    QLineEdit, QMessageBox, QFormLayout, QComboBox
from PyQt5.QtGui import QIcon, QPixmap, QFont, QColor


method_box_methods = ['Addition of all elements', 'Multiplication of all elements']


class Label(QLabel):
    clicked = pyqtSignal()
    doubleClicked = pyqtSignal()

    def __init__(self, parent=None):
        super(Label, self).__init__(parent)
        self.resize(75, 75)
        self.setText("Hello World")

    def mousePressEvent(self, event):
        if event.button() == Qt.LeftButton:
            self.clicked.emit()

    def mouseDoubleClickEvent(self, event):
        if event.button() == Qt.RightButton:
            self.doubleClicked.emit()


class Widget(QWidget):
    def __init__(self):
        super().__init__()
        self.setMinimumHeight(75)
        self.setMinimumWidth(75)                                            # +++

        self.label = Label(self)
        self.label.setWordWrap(True)
        self.color = QColor(255, 255, 255).name()
        self.label.setStyleSheet(f"background-color: {self.color}")
        self.label.clicked.connect(self.onClicked)
        self.label.doubleClicked.connect(self.onDoubleClicked)

        self.lineEdit = QLineEdit(self)
        self.lineEdit.editingFinished.connect(self.editFinished)
        self.lineEdit.setGeometry(self.label.geometry())
        self.lineEdit.hide()

    def onClicked(self):
        if self.color == '#ffd700':
            self.color = QColor(255, 255, 255).name()
        else:
            self.color = QColor(255, 215, 0).name()
        self.label.setStyleSheet(f"background-color: {self.color}")

    def onDoubleClicked(self):
        self.lineEdit.setText(self.label.text())
        self.lineEdit.setStyleSheet(f"background-color: {self.color}")
        self.lineEdit.show()
        self.lineEdit.setFocus()

    def editFinished(self):
        self.label.setText(self.lineEdit.text())
        self.lineEdit.hide()


class FormBuilder(QWidget):
    def __init__(self, parent=None):
        super().__init__(parent)

        self.create_button_forms()
        self.create_layouts()

    def create_button_forms(self):
        self.generate_button = QPushButton("Generate array")
#?        self.generate_button.setFixedHeight(30)
        self.clear_button = QPushButton("Clear array")
#?        self.clear_button.setFixedHeight(30)
        self.apply_button = QPushButton("Apply method")
#?        self.apply_button.setFixedHeight(30)
        self.method_box = QComboBox()
        self.method_box.addItems(method_box_methods)
#?        self.method_box.setFixedHeight(30)

    def create_layouts(self):
        layout = QVBoxLayout(self)
        layout.setContentsMargins(0, 0, 0, 0)                               # +++

        first_layer = QHBoxLayout()
        first_layer.addWidget(self.generate_button)
        first_layer.addWidget(self.clear_button)
        first_layer.addWidget(self.apply_button)

        second_layer = QHBoxLayout()
        second_layer.addWidget(self.method_box)

        layout.addLayout(first_layer)
        layout.addLayout(second_layer)


class MainWindow(QMainWindow):
    def __init__(self):
        super().__init__()
        self.centralWidget = QWidget()
        self.setCentralWidget(self.centralWidget)

        self.build_skeleton_with_basic_settings()
        self.create_and_connect_grid()

        self.create_array()

    def build_skeleton_with_basic_settings(self):
#?        self.setFixedSize(500, 550)
        self.resize(450, 550)                                               # +++
        self.setWindowTitle('Plates')
        self.setWindowIcon(QIcon('Images\\logo.jpg'))
        self.setFont(QFont('Arial', 16)) # убрать строку/заменить шрифт 

    def create_and_connect_grid(self):
        self.grid = QGridLayout(self.centralWidget)
        self.grid.setContentsMargins(20, 20, 20, 20)                        # +++
        self.formBuilder = FormBuilder()
#        self.grid.addWidget(self.formBuilder, 0, 0, Qt.AlignTop)
        self.grid.addWidget(self.formBuilder, 0, 0, 1, 5, Qt.AlignTop)      # +++

    def create_array(self):
        widget = Widget()
#        self.row, self.column = 0, 0
        self.row, self.column = 1, 0                                        # +++
        for i in range(5):
            self.grid.addWidget(widget, self.row, self.column) 
            self.column += 1
            widget = Widget()
            
        self.grid.setRowStretch(10, 1)                                      # +++
        

if __name__ == '__main__':
    app = QApplication(sys.argv)
    ex = MainWindow()
    ex.show()
    sys.exit(app.exec_())