Problem with equation numbering location

I have two very long equation but the problem is the number of the equation locating is wrong my code is, I now that the margin is 6 cm from the left but still it has to work my code looks like:

\documentclass [12pt]{article}
\usepackage{float}
%\usepackage{showframe}
\usepackage{authblk}
\usepackage{etoolbox}
\usepackage{amsmath}
\usepackage{graphicx}
\usepackage{subcaption}
\usepackage{tabularx,ragged2e,booktabs,caption}
\usepackage[utf8]{inputenc}
\usepackage[english]{babel}
\usepackage{caption}
\usepackage{amssymb}
\usepackage{graphicx,epstopdf}
\usepackage{caption}
\usepackage{graphicx,kantlipsum,setspace}
\usepackage{mathptmx}
\usepackage{pgfplots}
\captionsetup{font={stretch=1.0}}  %% this affects both figure and table
\setstretch{1.0}
\captionsetup{font=footnotesize}
\usepackage[left=6cm,top=3cm,right=2cm,bottom=3cm]{geometry}
\usepackage{lipsum}
\usepackage{setspace}
\usepackage{apacite}
\setstretch{1.5}

\newcolumntype{C}[1]{>{\Centering}m{#1}}
\renewcommand\tabularxcolumn[1]{C{#1}}
\newcommand\seqwlimits[3]{\{#1\}_{\mathstrut#2}^{\mathstrut#3}}

\renewcommand\Authfont{\fontsize{15}{1}\selectfont}

\begin{document}
$$\begin{split} Q_{G-Ind}(\theta= H\phi)& =-2log\bigg(\frac{L_T(\tilde{\theta})}{L_T(\hat{\theta})}\bigg)\\&= Q_{G-CC}(\theta= H p) - Q_{G-UC} (H\phi=H p)\\ & = \biggl(-2\biggl[L_T(\theta_0)-L_ T(\widehat{\theta})\biggr]\biggr) - \biggl(-2\biggl[L_T(\theta_0)-L_T(\tilde{\theta})\biggr]\biggr) \end{split}$$

and the other one is

$$M_{j+1} (d;p)= \frac{(1-p)(2j+1)+p(j-d+1)}{(j+1)\sqrt{1-p}} M_j(d;p)-\left(\frac{j}{j+1}\right) M_{j-1}(d;p),$$
\end{document}

• @phollox I missed the intention of the 'and the other ...' part. – albert Oct 24 '18 at 16:46
• Place of the number looks OK to me. The '(1)' is in the middle of the formula and the '(2)' doesn't fit anymore so it is placed on the next line. – albert Oct 24 '18 at 16:47
• the (1) is placed in the next line of all the equation lines – Hani Al Natour Oct 24 '18 at 16:48
• Can you share a picture of, the page with, the formula? Which engine are you using and which version of the distribution? – albert Oct 24 '18 at 17:00

Two solutions: either you reduce the left margin, if you can, or you remove the parentheses around the fraction j/j+1. I took the opportunity to remove multiply loaded packages, and incompatible packages, such as amssymb and mathptmx. I also suggest replacing the latter with the more complete newtx, based on the Times clone TeX Gyre Termes. Finally I set some delimiters to a smaller size (more adequate in my opinion):

\documentclass [12pt]{article}
\usepackage[utf8]{inputenc}
\usepackage[english]{babel}
\usepackage[left=6cm, right=2cm, vmargin=3cm, showframe]{geometry}
\usepackage{,setspace}
\usepackage{newtxtext, newtxmath}
\usepackage{amsmath}
\usepackage{float} %\usepackage{showframe}
\usepackage{etoolbox}
\usepackage{subcaption}
\usepackage{tabularx,ragged2e,booktabs,caption}
\usepackage{graphicx,epstopdf}
\usepackage{pgfplots}
\captionsetup{font={stretch=1.0}} %% this affects both figure and table \setstretch{1.0} \captionsetup{font=footnotesize}
\usepackage{apacite} \setstretch{1.5}


\providecommand\Authfont{\fontsize{15}{1}\selectfont}

\begin{document}

$$\begin{split} Q_{G-Ind}(\theta= H\phi) &=-2\log\biggl(\frac{L_T(\tilde{\theta})}{L_T(\hat{\theta})}\biggr) \\ &= Q_{G-CC}(\theta= H p) - Q_{G-UC} (H\phi=H p)\\ & = \Bigl(-2\Bigl[L_T(\theta_0)-L_ T(\widehat{\theta})\Bigr]\Bigr) - \Bigl(-2\Bigl[L_T(\theta_0)-L_T(\tilde{\theta})\Bigr]\Bigr) \end{split}$$
and the other one is
$$M_{j+1} (d;p)= \frac{(1-p)(2j+1)+p(j-d+1)}{(j+1)\sqrt{1-p}} M_j(d;p)-\frac{j}{j+1}M_{j-1}(d;p),$$

\end{document}