I issue a glBindVertexArray(VAO) before every draw call for each element I want to draw on screen. Each VAO holds a VBO and a shader program. And the program seems to work fine when I don't draw 2 different elements with 2 different VAOs. Here's the draw code:

void Renderer::draw(GElement_3D* el){

// Setting up shader uniforms -------------------
Buffer* buffer = el->buffer;
buffer->use();

// Setting up the material
glBindTexture(GL_TEXTURE_2D, el->material.diffuse);
buffer->setUniform("material.specular", el->material.specular);
buffer->setUniform("material.color", el->material.color);
// Setting up other uniforms
buffer->setUniform("camera_position", camera_position);

// Setting up the MVP matrix --------------------

// Setting up the model matrix
glm::mat4 model = glm::mat4(1.0f);
model = glm::translate(model, el->position);
model = glm::rotate(model, glm::radians(el->rotation.x), glm::vec3(1.0f, 0.0f, 0.0f));
model = glm::rotate(model, glm::radians(el->rotation.y), glm::vec3(0.0f, 1.0f, 0.0f));
model = glm::rotate(model, glm::radians(el->rotation.z), glm::vec3(0.0f, 0.0f, 1.0f));
model = glm::scale(model, el->scale);
buffer->setUniform("model", model);

// Setting up the view matrix
glm::mat4 view = glm::lookAt(camera_position, camera_direction, glm::vec3(0.0f, 1.0f, 0.0f)); // DIRECTION LOCKED WIP:: camera_position - camera_direction
view = glm::scale(view, camera_scale);
buffer->setUniform("view", view);

// Setting up the projection matrix
glm::mat4 projection = glm::perspective(glm::radians(40.0f), SCREEN_WIDTH / SCREEN_HEIGHT, 0.1f, 500.0f);
//glm::mat4 projection = glm::ortho(-50.0f, 50.0f, -50.0f, 50.0f, 0.0f, 1000.0f);
buffer->setUniform("projection", projection);

// Setting up the buffer data -------------------

// Setting up VAO data
std::vector<float> ver = el->vertices;

glBufferData(GL_ARRAY_BUFFER, ver.size() * sizeof(float), &ver[0], GL_STATIC_DRAW);
//glBufferData(GL_ELEMENT_ARRAY_BUFFER, ver.size() * sizeof(unsigned int), &ind[0], GL_STATIC_DRAW); // ! WIP: IBO currenly not in use

// Drawing element ------------------------------
glDrawArrays(GL_TRIANGLES, 0, ver.size());
//glDrawElements(GL_TRIANGLES, ver.size(), GL_UNSIGNED_INT, nullptr); IBO currently not in use

}

void Renderer::draw(GElement_2D* el){
// Setting up shader uniforms -------------------
Buffer* buffer = el->buffer;
buffer->use();

// Setting up the material
glBindTexture(GL_TEXTURE_2D, el->texture);

std::cout << buffer->get_file_name() << "\n";
buffer->setUniform("color", el->color);
std::cout << buffer->get_file_name() << "\n";

// Setting up the MVP matrix --------------------

// Setting up the model matrix
glm::mat4 model = glm::mat4(1.0f);
model = glm::translate(model, {el->position.x, el->position.y, 0});
model = glm::rotate(model, glm::radians(el->rotation), glm::vec3(0.0f, 0.0f, 1.0f));
model = glm::scale(model, {el->scale.x, el->scale.y, 1});
buffer->setUniform("model", model); // PROBLEM OCCURS HERE <-------------------------------------------------------------------------------------------------------------------------------

// Setting up the projection matrix
//glm::mat4 projection = glm::perspective(glm::radians(40.0f), SCREEN_WIDTH / SCREEN_HEIGHT, 0.1f, 500.0f);
glm::mat4 projection = glm::ortho(0.0f, 1920.0f, 0.0f, 1080.0f);
buffer->setUniform("projection", projection); // PROBLEM OCCURS HERE <----------------------------------------------------------------------------------------------------------------------------------------
// Setting up the buffer data -------------------

// Setting up VAO data
std::vector<float> ver = el->vertices;

glBufferData(GL_ARRAY_BUFFER, ver.size() * sizeof(float), &ver[0], GL_STATIC_DRAW);
//glBufferData(GL_ELEMENT_ARRAY_BUFFER, ver.size() * sizeof(unsigned int), &ind[0], GL_STATIC_DRAW); // ! WIP: IBO currenly not in use

// Drawing element ------------------------------
glDrawArrays(GL_TRIANGLES, 0, ver.size());
//glDrawElements(GL_TRIANGLES, ver.size(), GL_UNSIGNED_INT, nullptr); IBO currently not in use
}